Membrane-bound ribosomes in HeLa cells. I. Their proportion to total cell ribosomes and their association with messenger RNA

Selective Autophagy of the Protein Homeostasis Machinery: Ribophagy, Proteaphagy and ER-Phagy

The eukaryotic cell has developed intricate machineries that monitor and maintain proteome homeostasis in order to ensure cellular functionality. This involves the carefully coordinated balance between protein synthesis and degradation pathways, which are dynamically regulated in order to meet the constantly changing demands of the cell. Ribosomes, together with the endoplasmic reticulum (ER), are the key drivers of protein synthesis, folding, maturation and sorting, while the proteasome plays a pivotal role in terminating the existence of thousands of proteins that are misfolded, damaged or otherwise obsolete. The synthesis, structure and function of these dedicated machines has been studied for decades, however, much less is understood about the mechanisms that control and execute their own turnover. Autophagy, an evolutionarily conserved catabolic pathway, mediates degradation of a large variety of cytosolic substrates, ranging from single proteins to entire organelles or multi-subunit macromolecular complexes. In this review, we focus on selective autophagy of three key components of the protein homeostasis machinery: ribosomes, ER and proteasomes, through the selective autophagy pathways of ribophagy, ER-phagy, and proteaphagy. We discuss newly discovered mechanisms for the selective clearance of these substrates, which are often stress-dependent and involve specialized signals for cargo recognition by a growing number of receptors. We further discuss the interplay between these pathways and their biological impact on key aspects of proteome homeostasis and cellular function in health and disease.

Global, quantitative and dynamic mapping of protein subcellular localization

Subcellular localization critically influences protein function, and cells control protein localization to regulate biological processes. We have developed and applied Dynamic Organellar Maps, a proteomic method that allows global mapping of protein translocation events. We initially used maps statically to generate a database with localization and absolute copy number information for over 8700 proteins from HeLa cells, approaching comprehensive coverage. All major organelles were resolved, with exceptional prediction accuracy (estimated at >92%). Combining spatial and abundance information yielded an unprecedented quantitative view of HeLa cell anatomy and organellar composition, at the protein level. We subsequently demonstrated the dynamic capabilities of the approach by capturing translocation events following EGF stimulation, which we integrated into a quantitative model. Dynamic Organellar Maps enable the proteome-wide analysis of physiological protein movements, without requiring any reagents specific to the investigated process, and will thus be widely applicable in cell biology.

DOI:http://dx.doi.org/10.7554/eLife.16950.001

The interior of every cell is highly organised, and contains many compartments, called organelles, that are dedicated to specific roles. Proteins are the tools and machines of the cell, and each organelle has its own set of proteins that it requires to work correctly. Each cell contains ten or more organelles, and several thousand different types of proteins. The exact location of proteins in the cell is important; once we know what compartment a protein is in, it is easier to narrow down what it might be doing.

The location of many proteins in a cell is unclear or simply not known. Moreover, since changing the location of a protein can change its activity, it is also important to be able to detect changes in the location of proteins under different circumstances, such as before and after drug treatment.

Itzhak et al. set out to develop a method that reveals the locations of all the proteins in a cell at any given time. The resulting technique maps the location of most of the proteins in a human cancer cell line and, in addition, determines how many copies of each protein there are. Combining these two types of information produces a model of the cell’s architecture. Importantly, Itzhak et al. were able to compare such a model of the cell under normal circumstances to a model made after the cell had been stimulated with a growth factor. This revealed which proteins had changed location, identifying these proteins as important for the cell’s response to the growth factor.

The new mapping method could be used in the future to analyse the anatomy of different cell types, such as nerve cells and cells of the immune system. Itzhak et al. also want to investigate the differences between healthy cells and cells from people with neurological disorders to understand how such diseases arise.

DOI:http://dx.doi.org/10.7554/eLife.16950.002

Eukaryotic GCP1 is a conserved mitochondrial protein required for progression of embryo development beyond the globular stage in Arabidopsis thaliana

GCPs (glycoproteases) are members of the HSP70 (heat-shock protein 70)/actin ATPase superfamily that are highly conserved in taxonomically diverse species from bacteria to man, suggesting an essential physiological role. Although originally identified and annotated as putative endopeptidases, a proteolytic activity could not be confirmed for these proteins. Our survey of genome databases revealed that all eukaryotic organisms contain two GCP genes [called GCP1 and GCP2/Kae1 (kinase-associated endopeptidase 1)], whereas prokaryotes have only one, either of the GCP1- (Bacteria) or the GCP2/Kae1- (Archaea) type. GCP2/Kae1 is essential for telomere elongation and transcription of essential genes, although little is known about the localization, expression and physiological role of GCP1. In the present study on GCP1-type proteins from eukaryotic organisms we demonstrated that GCP1 is a mitochondrial protein in Homo sapiens [called here GCP1/OSGEPL1 (O-sialoglycoprotein endopeptidase)] and Arabidopsis thaliana, which is located/anchored to the mitochondrial inner membrane. Analysis of mRNA and protein levels revealed that the expression of GCP1/OSGEPL1 in A. thaliana and H. sapiens is tissue- and organ-specific and depends on the developmental stage, suggesting a more specialized function for this protein. We showed that homozygous A. thaliana GCP1 T-DNA (transferred DNA) insertion lines were embryonic lethal. Embryos in homozygous seeds were arrested at the globular stage and failed to undergo the transition into the heart stage. On the basis of these data we propose that the mitochondrial GCP1 is essential for embryonic development in plants.

Nuclear inheritance of erythromycin resistance in human cells: new class of mitochondrial protein synthesis mutants

The characterization of two new erythromycin-resistant mutants of HeLa cells is described. The strains ERY2305 and ERY2309 both exhibited resistance to erythromycin in growth assays and cell-free mitochondrial protein synthesis assays. The erythromycin resistance phenotype could not be transferred by cybridization. The mutation appeared to be encoded in the nucleus and inherited as a recessive trait. These two mutants, therefore, represent a new class of erythromycin-resistant mutants in human cells that is distinct from the cytoplasmically inherited mutation in strain ERY2301 described previously.

The pathogenic A3243G mutation in human mitochondrial tRNALeu(UUR) decreases the efficiency of aminoacylation

Mutations of mtDNA, particularly those in mtDNA-encoded tRNA genes, are emerging as a significant cause of human disease. We examined the effects of the pathogenic A3243G and T3271C mutations in the mitochondrial tRNA(Leu(UUR)) gene on the aminoacylation of tRNA(Leu(UUR)). Transmitochondrial cells carrying these mutations have decreased steady-state levels of mitochondrial tRNA(Leu(UUR)). The A3243G mutation also results in a decrease in the fraction of aminoacylated tRNA(Leu(UUR)). To determine if the decreased fraction of aminoacylated tRNA(Leu(UUR)) in A3243G mutant cells was due to a defect in the ability of mutant tRNA to be aminoacylated by the human mitochondrial leucyl-tRNA synthetase, we examined the aminoacylation kinetics of wild-type and mutant tRNA(Leu(UUR)), using both native and in vitro transcribed tRNA(Leu(UUR)). Native A3243G mutant tRNA(Leu(UUR)) was 25-fold less efficiently aminoacylated in vitro, compared to native wild-type tRNA(Leu(UUR)). The T3271C mutation in tRNA(Leu(UUR)) did not affect the efficiency of aminoacylation of the native tRNA. There were no differences in aminoacylation efficiencies among wild-type and mutant tRNA(Leu(UUR)) transcripts. The combined effects of the reductions in the steady-state levels and the aminoacylated fraction of tRNA(Leu(UUR)) are likely to contribute to the decreases in the rates of mitochondrial translation observed in mutant cells. These results also suggest that the A3243G and T3271C mutations may have distinct mechanisms of pathogenesis.

Comparative proteomics as a new tool for exploring human mitochondrial tRNA disorders

More than 70 different point mutations in human mitochondrial tRNA genes are correlated with severe disorders, including fatal cardiopathies, encephalopathies, myopathies, and others. So far, investigation of the molecular impact(s) of mutations has focused on the affected tRNA itself by seeking structural and/or functional perturbations capable of interfering with synthesis of the 13 mitochondrion-encoded subunits of respiratory chain complexes. Here, a proteomic approach was used to investigate whether such mutations would affect the pattern of mitochondrial proteins at a broader level. Analysis of several hundred mitochondrial proteins from sibling cybrid cell lines by two-dimensional electrophoresis, an approach that takes into account all regulatory steps of mitochondrial and nuclear gene expression, indeed reveals a number of up- and downregulated proteins when healthy and single-point-mutation-carrying mitochondria representative of either MELAS or MERRF syndrome were compared. Assignment by mass spectrometry of the two proteins which exhibit obvious large quantitative decreases in the levels of both pathologic mitochondria identified nuclear-encoded subunits of cytochrome c oxidase, a respiratory chain complex. This clearly shows a linkage between the effects of mutations in mitochondrial tRNA genes and the steady-state level of nuclear-encoded proteins in mitochondria. It opens new routes toward a large-scale exploration of potential proteic partners involved in the genotype-phenotype correlation of mitochondrial disorders.

Prenatal diagnosis of NADH:ubiquinone oxidoreductase deficiency

NADH:ubiquinone oxidoreductase (complex I of the mitochondrial respiratory chain) deficiency is a severe disorder with an often early fatal outcome. Prenatal diagnosis for complex I defects currently relies mainly on biochemical assays of complex I in fetal tissues such as chorionic villi (CV), and is only in a minority of cases possible by means of mutational analysis of nuclear-encoded genes of complex I. We report on our experience to date with prenatal diagnosis in pregnancies at risk for complex I deficiency. We measured complex I activity in native CV and/or cultured CV in 23 pregnancies in 15 families. In accordance with the results of the investigations in CV, 15 children were born clinically unaffected. Two prenatally diagnosed unaffected fetuses and two prenatally diagnosed affected fetuses were lost prematurely with spontaneous or provoked abortions, respectively. Two affected children were born (prenatally found to be affected). In two pregnancies a discrepancy between native and cultured cells was found. We conclude that prenatal diagnosis for complex I deficiency can be reliably performed. Pitfalls were encountered in using cultured CV as a result of maternal cell contamination (MCC). Future research on pathogenic nuclear mutations underlying complex I deficiency will extend the possibilities for prenatal diagnosis at the molecular level.

Human NADH:ubiquinone oxidoreductase

NADH:ubiquinone oxidoreductase consists of at least 43 proteins; seven are encoded by the mitochondrial genome, while the remainder are encoded by the nuclear genome. A deficient activity of this enzyme complex is frequently observed in the clinical heterogeneous group of mitochondrial disorders, with Leigh (-like) disease as the main contributor. Enzyme complex activity measurement in skeletal muscle is the mainstay of the diagnostic process. Fibroblast studies are a prerequisite whenever prenatal enzyme diagnosis is considered. Mitochondrial DNA mutations are found in approximately 5-10% of all complex I deficiencies. Recently, all structural nuclear complex I genes have been determined at the cDNA level and several at the gDNA level. A comprehensive mutational analysis study of all complex I nuclear genes in a group of 20 patients exhibiting this deficiency revealed mutations in about 40%. Here, we describe the enzymic methods we use and the recent progress made in genomics and cell biology of human complex I.

Search for differences in post-transcriptional modification patterns of mitochondrial DNA-encoded wild-type and mutant human tRNALys and tRNALeu(UUR)

Post-transcriptional modifications are characteristic features of tRNAs and have been shown in a number of cases to influence both their structural and functional properties, including structure stabilization, amino-acylation and codon recognition. We have developed an approach which allows the investigation of the post-transcriptional modification patterns of human mitochondrial wild-type and mutant tRNAs at both the qualitative and the quantitative levels. Specific tRNA species are long-term labeled in vivo with [32P]orthophosphate, isolated in a highly selective way, enzymatically digested to mononucleotides and then subjected to two-dimensional thin layer chromatographic analysis. The wild-type tRNALysand the corresponding tRNALyscarrying the A8344G mutation associated with the MERRF (Myoclonic Epilepsy with Ragged Red Fibers) syndrome exhibit the same modified nucleotides at the same molar concentrations. By contrast, a quantitatively different modification pattern was observed between the wild-type tRNALeu(UUR)and its counterpart carrying the A3243G mutation associated with the MELAS (Mitochondrial Myopathy, Encephalopathy with Lactic Acidosis and Stroke-like episodes) syndrome, the latter exhibiting a 50% decrease in m2G content. Complementary sequencing of tRNALeu(UUR)has allowed the localization of this modification at position 10 within the D-stem of the tRNA. The decreased level of this modification may have important implications for understanding the molecular mechanism underlying the MELAS-associated mitochondrial dysfunction.

Evidence for the presence of 5S rRNA in mammalian mitochondria

Mammalian mitochondrial ribosomes contain two prokaryotic-like rRNAs, 12S and 16S, both encoded by mitochondrial DNA. As opposed to cytosolic ribosomes, however, these ribosomes are not thought to contain 5S rRNA. For this reason, it has been unclear whether 5S rRNA, which can be detected in mitochondrial preparations, is an authentic organellar species imported from the cytosol or is merely a copurifying cytosol-derived contaminant. We now show that 5S rRNA is tightly associated with highly purified mitochondrial fractions of human and rat cells and that 5S rRNA transcripts derived from a synthetic gene transfected transiently into human cells are both expressed in vivo and present in highly purified mitochondria and mitoplasts. We conclude that 5S rRNA is imported into mammalian mitochondria, but its function there still remains to be clarified.

Respiration and growth defects in transmitochondrial cell lines carrying the 11778 mutation associated with Leber's hereditary optic neuropathy

Mitochondrial DNA from two genetically unrelated patients carrying the mutation at position 11778 that causes Leber's hereditary optic neuropathy has been transferred with mitochondria into human mtDNA-less rho0206 cells. As analyzed in several transmitochondrial cell lines thus obtained, the mutation, which is in the gene encoding subunit ND4 of the respiratory chain NADH dehydrogenase (ND), did not affect the synthesis, size, or stability of ND4, nor its incorporation into the enzyme complex. However, NADH dehydrogenase-dependent respiration, as measured in digitonin-permeabilized cells, was specifically decreased by approximately 40% in cells carrying the mutation. This decrease, which was significant at the 99.99% confidence level, was correlated with a significantly reduced ability of the mutant cells to grow in a medium containing galactose instead of glucose, indicating a clear impairment in their oxidative phosphorylation capacity. On the contrary, no decrease in rotenone-sensitive NADH dehydrogenase activity, using a water-soluble ubiquinone analogue as electron acceptor, was detected in disrupted mitochondrial membranes. This is the first cellular model exhibiting in a foreign nuclear background mitochondrial DNA-linked biochemical defects underlying the optic neuropathy phenotype.

MtDNA mutation in MERRF syndrome causes defective aminoacylation of tRNA(Lys) and premature translation termination

We have investigated the pathogenetic mechanism of the mitochondrial tRNA(Lys) gene mutation (position 8344) associated with MERRF encephalomyopathy in several mitochondrial DNA (mtDNA)-less cell transformants carrying the mutation and in control cells. A decrease of 50-60% in the specific tRNA(Lys) aminoacylation capacity per cell was found in mutant cells. Furthermore, several lines of evidence reveal that the severe protein synthesis impairment in MERRF mutation-carrying cells is due to premature termination of translation at each or near each lysine codon, with the deficiency of aminoacylated tRNA(Lys) being the most likely cause of this phenomenon.

In vitro analysis of mutations causing myoclonus epilepsy with ragged-red fibers in the mitochondrial tRNA(Lys)gene: two genotypes produce similar phenotypes

Cytoplasts from patients with myoclonus epilepsy with ragged-red fibers harboring a pathogenic point mutation at either nucleotide 8344 or 8356 in the human mitochondrial tRNA(Lys) gene were fused with human cells lacking endogenous mitochondrial DNA (mtDNA). For each mutation, cytoplasmic hybrid (cybrid) cell lines containing 0 or 100% mutated mtDNAs were isolated and their genetic, biochemical, and morphological characteristics were examined. Both mutations resulted in the same biochemical and molecular genetic phenotypes. Specifically, cybrids containing 100% mutated mtDNAs, but not those containing the corresponding wild-type mtDNAs, exhibited severe defects in respiratory chain activity, in the rates of protein synthesis, and in the steady-state levels of mitochondrial translation products. In addition, aberrant mitochondrial translation products were detected with both mutations. No significant alterations were observed in the processing of polycistronic RNA precursor transcripts derived from the region containing the tRNA(Lys) gene. These results demonstrate that two different mtDNA mutations in tRNA(Lys), both associated with the same mitochondrial disorder, result in fundamentally identical defects at the cellular level and strongly suggest that specific protein synthesis abnormalities contribute to the pathogenesis of myoclonus epilepsy with ragged-red fibers.

Interaction between mRNA, ribosomes and the cytoskeleton

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Bacteriophage T4 gene 32 protein shares antigen determinants with reconstituted HeLa hnRNP proteins in western blots

A polyclonal antiserum against purified bacteriophage T4 gene 32 protein was raised in rabbits. In Western blots it detected a number of SDS-PAGE separated nuclear and ribosomal proteins of HeLa cells. Using a renaturing blotting system, however, larger hnRNP proteins ranging between 66.000 and 82.000 Da preferentially reacted with this antiserum. In addition hnRNP group A core proteins were detected to a minor extent. Nucleic acid binding proteins like histones or ribosomal proteins were not stained by this antibody after renaturation.

Effects of mycoplasma contamination on phenotypic expression of mitochondrial mutants in human cells

HeLa cells sensitive to the mitochondrial protein synthesis inhibitors erythromycin (ERY) and chloramphenicol (CAP) and HeLa variants resistant to the effects of these drugs were purposefully infected with drug-sensitive and -resistant mycoplasma strains. Mycoplasma hyorhinis and the ERY-resistant strain of Mycoplasma orale, MO-ERYr, did not influence the growth of HeLa and ERY-resistant ERY2301 cells in the presence or absence of ERY. M. hyorhinis also did not affect the growth of HeLa and CAP-resistant Cap-2 cells in the presence or absence of CAP. However, both HeLa and Cap-2 cells infected with the CAP-resistant strain of M. hyorhinis, MH-CAPr, were more sensitive to the cytotoxic effect of CAP. This may be due to the glucose dependence of the cells, which was compromised by the increased utilization of glucose by MH-CAPr in these infected cell cultures. In vitro protein synthesis by isolated mitochondria was significantly altered by mycoplasma infection of the various cell lines. A substantial number of mycoplasmas copurified with the mitochondria, resulting in up to a sevenfold increase in the incorporation of [3H]leucine into the trichloroacetic acid-insoluble material. More importantly, the apparent drug sensitivity or resistance of mitochondrial preparations from mycoplasma-infected cells reflected the drug sensitivity or resistance of the contaminating mycoplasmas. These results illustrate the hazards in interpreting mitochondrial protein synthesis data derived from mycoplasma-infected cell lines, particularly putative mitochondrially encoded mutants resistant to inhibitors of mitochondrial protein synthesis.

The preparative isolation of mitochondria from Chinese hamster ovary cells

A "hybrid" discontinuous gradient consisting of 6% Percoll overlaid on metrizamide separated mitochondria from other organelles in a Chinese hamster ovary cell postnuclear supernatant in a single 15-min centrifugation. The mitochondrial preparation contained about 25% of the mitochondrial marker, cytochrome-c oxidase, in a form that was about 90% latent. Based on the postnuclear supernatant, cytochrome-c oxidase activity was enriched approximately 45-fold. Trace amounts of lysosomal, rough endoplasmic reticular, Golgi, peroxisomal, plasma membrane, and cytosolic markers were found in the preparation. Electron microscopy revealed that the preparation consisted almost exclusively of mitochondria with only minor amounts of contaminating organelles. Analysis of the mitochondrial preparation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis demonstrated that the mitochondrial preparation had a unique protein profile compared to the postnuclear supernatant and other gradient interfaces. Separation of the mitochondria into membrane and lumenal (matrix) fractions by treatment with 100 mM Na2CO3, pH 11.5, also indicated that the mitochondria were intact; they were rich in lumenal proteins. The data indicate that the mitochondria represent maximally about 2.2% of Chinese hamster ovary cell postnuclear supernatant protein. These isolated mitochondria should prove useful for problems in molecular cell biology.

Translational initiation factor and ribosome association with the cytoskeletal framework fraction from HeLa cells

The association of mRNA and ribosomes with the cytoskeleton of eucaryotic cells may be important for protein synthesis and its regulation. HeLa cells were gently lysed with detergent, and soluble and cytoskeletal framework subfractions were prepared by centrifugation. We analyzed these fractions for ribosomes and confirmed earlier findings that polysomes are preferentially associated with the cytoskeletal fraction. The levels of initiation factors eIF-2, eIF-3, eIF-4A, and eIF-4B were quantitated by immunoblotting; all are enriched in the cytoskeletal fraction relative to the soluble fraction. Heat shock, fluoride, pactamycin , and cytochalasin caused the release of both ribosomes and initiation factors into the soluble fraction. However, treatment of the cytoskeletal fraction with EDTA or low levels of ribonuclease resulted in polysome degradation but no release. Therefore initiation factor association with the cytoskeletal framework correlates with the presence of ribosomes, whereas ribosome association does not require intact mRNA.

Mammalian mitochondrial mutants selected for resistance to the cytochrome b inhibitors HQNO or myxothiazol

Mouse LA9 cell lines were selected for increased resistance to either HQNO or myxothiazol, inhibitors of electron transport which bind to the mitochondrial cytochrome b protein. Two phenotypically distinguishable HQNO-resistant mutants were recovered while the myxothiazol-resistant isolates had a common phenotype. All three mutant phenotypes were transmitted cytoplasmically in cybrid crosses. Biochemical studies further established that for all three mutant types, resistance at the cellular level was paralleled by an increase in inhibitor resistance of mitochondrial succinate-cytochrome c oxidoreductase, the respiratory complex containing cytochrome b. As with the previously described mitochondrial antimycin-resistant mutant, the initial biochemical and genetic studies indicated that these mutations occur within the mitochondrial cytochrome b gene. This conclusion was strongly supported by the results of mtDNA restriction fragment analyses in which it was found that one HQNO-resistant mutant had undergone a small insertion or duplication in the apocytochrome b gene. Finally, all four mitochondrial cytochrome b mutants have been analyzed in both cell plating studies and succinate-cytochrome c oxidoreductase assays to determine the pattern of cross-resistance to inhibitors of cytochrome b other than the one used for selection.

Mitochondrial genetics of mammalian cells: a mouse antimycin-resistant mutant with a probable alteration of cytochrome b

Mouse LA9 antimycin-resistant mutants (ANT-R) were isolated and characterized. Genetic analyses established that this phenotype is encoded within the mtDNA: (1) the ANT-R phenotype showed frequent mitotic segregation and reassortment in hybrid clonal lines; (2) it was transmitted directly in cybrid crosses; and (3) it was cotransmitted in cybrid crosses with the mitochondrial CAP-R marker. Furthermore, the genetic studies suggested that the LA9 CAP-R ANT-R cells were heteroplasmic and contained at least two mtDNA genotypes, cap-r ant-s and cap-s ant-r. Cellular respiration of the ANT-R mutant was markedly more resistant to inhibition by antimycin than that of the parental ANT-S cells. The increased resistance of cellular respiration was entirely accounted for by an increase in the resistance of mitochondrial succinate-cytochrome c oxidoreductase to antimycin inhibition. There was no detectable change in the specific activity of the oxidoreductase in mitochondria of resistant ANT-R cells nor in the sensitivity of the complex to three other specific inhibitors of the complex: TTFA, myxothiazol, and HQNO. Taken together, these studies indicate that the ANT-R phenotype is most likely encoded within the mitochondrial cytochrome b gene and, more specifically, within an antimycin binding domain.

Human cell variants resistant to methylglyoxal-bis(guanylhydrazone) display increased sensitivity to chloramphenicol

Four variants of the cultured human cell line VA2 have been isolated which are resistant to the antiproliferative and antimitochondrial effects of methylglyoxal-bis(guanylhydrazone) (MGBG). Each of the four variants is two- to fivefold more sensitive to the mitochondrial protein synthesis inhibitor chloramphenicol (CAP) than wild type when grown in the absence of MGBG, and five- to tenfold more sensitive to CAP when grown in the presence of MGBG. Uptake studies demonstrate that each MGBG-resistant variant cell line is freely permeable to CAP. The in vivo rates of mitochondrial protein synthesis are significantly reduced in each of the variants whether pregrown and labeled in the presence or absence of MGBG. When cytoplasts from a cytoplasmically inherited CAP-resistant mutant are fused to an MGBG-resistant recipient cell line, cybrid clones can be isolated which are functionally resistant to low levels of CAP. With continued growth, the levels of resistance to CAP do not, however, approach the levels of resistance of the CAP-resistant donor cell line. When CAP resistance is subsequently transferred from a CAP/MGBG-resistant cybrid by enucleation and fusion to other human cell lines, then CAP-resistant cybrids can be readily selected in high levels of CAP. It is possible that the substantial decrease in mitochondrial protein synthesis observed in the variants fully accounts for their increased sensitivity to CAP, although the basis for this decreased rate of mitochondrial protein synthesis is not understood.

In situ photochemical crosslinking of HeLa cell mitochondrial DNA by a psoralen derivative reveals a protected region near the origin of replication

The in vivo association with proteins of HeLa cell mitochondrial DNA (mtDNA) has been investigated by analyzing the pattern of in situ crosslinking of the DNA by 4'-hydroxymethyl-4, 5',8-trimethylpsoralen (HMT). Either isolated mitochondria or whole cells were irradiated with long wavelength UV light in the presence of ths psoralen derivative, and the mtDNA was then isolated and analyzed in the electron microscope under totally denaturing conditions. No evidence of nucleosomal structure was found. The great majority of the molecules (approximately 90%) had a double-stranded DNA appearance over most of their contour length, with one to several bubbles occupying the rest of the contour, while the remaining 10% of the molecules appeared to be double-stranded over their entire length. Analysis of restriction fragments indicated the presence, in approximately 80% of the molecules, of a protected segment (300 to 1500 bp long) in a region which was centered asymmetrically around the origin of replication so as to overlap extensively the D-loop. Control experiments showed that at most 30% of the bubbles found near the origin could represent D-loops or expanded D-loops: furthermore, it could be excluded that some sequence peculiarity would account for the preferential location of bubbles near the origin of replication. The data have been interpreted to indicate that, in at least 55% of HeLa cell mtDNA molecules, the region around the origin is protected from in situ psoralen crosslinking by proteins or protein complexes which are associated in vivo with the DNA.

Effects of mycoplasma contamination on phenotypic expression of mitochondrial mutants in human cells

HeLa cells sensitive to the mitochondrial protein synthesis inhibitors erythromycin (ERY) and chloramphenicol (CAP) and HeLa variants resistant to the effects of these drugs were purposefully infected with drug-sensitive and -resistant mycoplasma strains. Mycoplasma hyorhinis and the ERY-resistant strain of Mycoplasma orale, MO-ERYr, did not influence the growth of HeLa and ERY-resistant ERY2301 cells in the presence or absence of ERY. M. hyorhinis also did not affect the growth of HeLa and CAP-resistant Cap-2 cells in the presence or absence of CAP. However, both HeLa and Cap-2 cells infected with the CAP-resistant strain of M. hyorhinis, MH-CAPr, were more sensitive to the cytotoxic effect of CAP. This may be due to the glucose dependence of the cells, which was compromised by the increased utilization of glucose by MH-CAPr in these infected cell cultures. In vitro protein synthesis by isolated mitochondria was significantly altered by mycoplasma infection of the various cell lines. A substantial number of mycoplasmas copurified with the mitochondria, resulting in up to a sevenfold increase in the incorporation of [3H]leucine into the trichloroacetic acid-insoluble material. More importantly, the apparent drug sensitivity or resistance of mitochondrial preparations from mycoplasma-infected cells reflected the drug sensitivity or resistance of the contaminating mycoplasmas. These results illustrate the hazards in interpreting mitochondrial protein synthesis data derived from mycoplasma-infected cell lines, particularly putative mitochondrially encoded mutants resistant to inhibitors of mitochondrial protein synthesis.

Uniparental propagation of mitochondrial DNA in mouse-human cell hybrids

The retention of the two parental mitochondrial DNAs has been investigated in a large number of mouse-human cell hybrids segregating either mouse or human chromosomes, by using a highly sensitive and specific method for detection of the DNA; the results have been correlated with the karyotype and isozyme marker pattern in the same hybrid lines. In all the hybrids examined, a consistent pattern was observed for the type of mitochondrial DNA retained: the mitochondrial DNA of the parent whose chromosomes were segregated from the nucleus was undetectable or present in marginal amounts. This was true also of hybrids containing a complete set of the segregating chromosomes in the total or a large fraction of the cell population.

Mitochondrial protein synthesis in Chinese hamster cells (line CHO) synchronized by isoleucine deprivation

Mitochondrial protein synthesis was measured in line CHO cells after phases of the cell cycle were synchronized by isoleucine deprivation or mitotic selection. Maximum incorporation of [3H] leucine into mitochondrial polypeptides occurred within 2 hours after isoleucine was added to initiate G1 traverse. In cells synchronized in G1 by mitotic selection, the rate of mitochondrial protein synthesis was fairly constant throughout the cell cycle. SDS-polyacrylamide gel electrophoretic profiles of labeled mitochondrial polypeptides were similar in cells synchronized by either isoleucine deprivation or mitotic selection. Obvious changes in the distribution of polypeptides were not detected during various phases of the cell cycle. The increased rate of incorporation of [3H] leucine into mitochondrial polypeptides after reversal of G1-arrest may indicate that mitochondrial protein synthesis and possibly mitochondrial biogenesis are synchronized in CHO cells deprived of isoleucine.

[Study of the regulation of plastid development in Euglena gracilis. II. Functional localisation and synthesis of ribosomal chloroplast particles (author's transl)]

Chloroplast ribosomes in greening cells of Euglena gracilis are found either in the stroma or bound to thylakoid membranes. The membrane-bound chloroplast ribosomes are of two main types: those which can be released by 0.5 M KCl or by puromycin and 0.5 M KCl, and those which are released by detergent (deoxycholate or Triton X-100) and KCl. The ribosomes which are released by puromycin are presumably bound to chloroplast membrane by nascent peptide chains. Ribosomes released by puromycin are found only during the course of plastidial differentiation at the time of active thylacoid membrane synthesis. Following greening, those ribosomes remain bound to the membranes but can be removed by KCl alone. An analysis of RNA labelling showed that 30-S but not 53-S subunits of membrane-bound ribosomes are of uniform specific activity. This suggests that 30-S subunit exchange in a common pool while 53 S subunits remain membrane bound and do not exchange in a common pool. Membrane-bound chloroplast ribosomes which are released either by puromycin or by detergent are originally derived from loosely bound particles, released by 0.5 M KCl.

Cytoplasmically inherited mutations of a human cell line resulting in deficient mitochondrial protein synthesis

A large number of mutants deficient in mitochondrial protein synthesis (mtPS-) have been isolated from the human cell line VA2-B by subjecting cells partially depleted of their mtDNA to mutagenic treatments thought to be specific for mtDNA. Each of these mtPS- mutants has less than 10% of the wild-type rate of mitochondrial protein synthesis, exhibits reduced cytochrome oxidase and rutamycin sensitive ATPase activities, requires high concentrations of glucose, and grows indefinitely in the presence of 100 micrograms/ml of chloramphenicol (CAP). Fusion of cytoplasts from seven mtPS- mutants to the nucleated thioguanine-resistant VA2-B derivative TG-6 has yielded numerous cybrid clones which grow in CAP plus thioguanine, whereas almost no clones have resulted from the fusion of nucleated mtPS- cells to TG-6 cells: these results suggest that the gene(s) coding for the phenotype of mtPS- cells is localized in the cytoplasm (mtDNA?).

Reversible tenfod reduction in mitochondria DNA content of human cells treated with ethidium bromide

Cells of the human line VA2-B in suspension culture have been treated with very low concentrations of ethidium bromide for the purpose of reducing the amount of mitochondrial DNA (mit-DNA) per cell. Cells maintained in the presence of 5 ng/ml ethidium bromide grew at a normal rate for three days; thereafter, their doubling time gradually increased to a stable value of about 60 h. In these cells, the rate of 3H thymidine incorporation into mit-DNA decreased very rapidly to approximately 60% of the normal, and remained thereafter at this level, while the amount of mit-DNA per cell stabilized around a level of 70--80% of the control. In cells long-term treated with 5 ng/ml ethidium bromide, the rate of mitochondrial protein synthesis was about 35% of the normal, and the cytochrome c oxidase activity about 50% of the control. Cells treated with 20 ng/ml of the drug underwent 3--4 cell doublings at control rates, then gradually stopped growing, and eventually died. In these cells, the rate of incorporation of 3H thymidine into mit-DNA was reduced to 50% of the control value after 10 min treatment with ethidium bromide, and became barely detectable after three cell doublings. At this time, the cells had on the average less than 10% of the control amount of mit-DNA, the rate of mitochondrial protein synthesis was reduced to 3% of the normal, and the specific activities of cytochrome c oxidase and rutamycin-sensitive ATPase were less than 20% of the control values. In spite of these marked changes, the cells exhibited only a 20--30% loss in cell viability, as estimated by cloning efficiency, after three days of exposure to the drug. Cells treated with ethidium bromide at 20 ng/ml for three days, and then transferred to drug-free medium, recovered a near-to-normal growth rate and cloning efficiency and a near-to-normal rate of synthesis and amount of mit-DNA in about five days.

Biochemical and electron microscopic characterization of DNA-RNA complexes from HeLa cell mitochondria

The previous electron microscopic investigations on the occurrence in HeLa cell mitochondria of transcription complexes of mitochondrial DNA [Aloni, Y., and Attardi, G. (1972a), J. Mol. Biol. 70, 363-373] have been extended with the aim of obtaining these complexes in a reasonably pure form for biochemical analysis. By using conditions designed to minimize losses of such structures and any possible contamination by nuclear DNA, it has been shown that a substantial fraction (40 to 50%) of mitochondrial DNA can be isolated from exponentially growing HeLa cells in the form of fastsedimenting complexes with RNA. These complexes have been characterized with respect to density and sedimentation properties, content in newly synthesized RNA, stability of the association of RNA with DNA, presence of different forms of mitochondrial DNA, and electron microscopic appearance. The properties of these complexes, as well as the results of reconstruction experiments, strongly suggest that the majority of such structures represent true transcriptional intermediates. The occurrence in this fraction of replicating or newly replicated mitochondrial DNA molecules has been observed. Although the presence of single-stranded DNA segments makes the replicative intermediates particularly susceptible to aggregation with free RNA, electron microscopic observations point to the possibility that these intermediates may be recruited for transcription.

Failure to detect "cap" structures in mitochondrial DNA-coded poly(A)-containing RNA from HeLa cells

The structure of the 5'-termini has been investigated in mitochondrial DNA-coded poly(A)-containing RNA from HeLa cells. For this purpose, mitochondrial RNA isolated from cells labeled for 3 hours with [32P]orthophosphate in the presence of 20 microgram/ml camptothecin, and selected for poly(A) content by two passages through oligo(dT)-cellulose, was digested either with the nuclease P1 or with a mixture of RNases: the digestion products were then fractionated by two-dimensional electrophoresis. No "cap" structures were detected under conditions where the presence of such structures in one out of five to ten RNA molecules would have been recognized. It is, therefore, likely that "cap" structures are completely absent in HeLa cell mitochondrial poly(A)-containing RNA.

Comparison between the ribosomal ribonucleic acids from free and membrane-bound ribosomal fractions of HeLa cells

The rRNA species from the total cytoplasmic, free and membrane-bound fractions of HeLa cells were compared. With the use of T1 ribonuclease and combined T1 ribonuclease plus pancreatic ribonuclease 'fingerprinting' procedures, no significant differences were found between the rRNA species from the different subcellular fractions.