Expression of the mitochondria genome in HeLa cells. IV. Titration of mitochondrial genes for 16 s, 12 s and 4 s RNA

Structural and Molecular Basis for Mitochondrial DNA Replication and Transcription in Health and Antiviral Drug Toxicity

Human mitochondrial DNA (mtDNA) is a 16.9 kbp double-stranded, circular DNA, encoding subunits of the oxidative phosphorylation electron transfer chain and essential RNAs for mitochondrial protein translation. The minimal human mtDNA replisome is composed of the DNA helicase Twinkle, DNA polymerase γ, and mitochondrial single-stranded DNA-binding protein. While the mitochondrial RNA transcription is carried out by mitochondrial RNA polymerase, mitochondrial transcription factors TFAM and TFB2M, and a transcription elongation factor, TEFM, both RNA transcriptions, and DNA replication machineries are intertwined and control mtDNA copy numbers, cellular energy supplies, and cellular metabolism. In this review, we discuss the mechanisms governing these main pathways and the mtDNA diseases that arise from mutations in transcription and replication machineries from a structural point of view. We also address the adverse effect of antiviral drugs mediated by mitochondrial DNA and RNA polymerases as well as possible structural approaches to develop nucleoside reverse transcriptase inhibitor and ribonucleosides analogs with reduced toxicity.

Mitochondrial DNA: Epigenetics and environment

Maintenance of the mitochondrial genome is essential for proper cellular function. For this purpose, mitochondrial DNA (mtDNA) needs to be faithfully replicated, transcribed, translated, and repaired in the face of constant onslaught from endogenous and environmental agents. Although only 13 polypeptides are encoded within mtDNA, the mitochondrial proteome comprises over 1500 proteins that are encoded by nuclear genes and translocated to the mitochondria for the purpose of maintaining mitochondrial function. Regulation of mtDNA and mitochondrial proteins by epigenetic changes and post-translational modifications facilitate crosstalk between the nucleus and the mitochondria and ultimately lead to the maintenance of cellular health and homeostasis. DNA methyl transferases have been identified in the mitochondria implicating that methylation occurs within this organelle; however, the extent to which mtDNA is methylated has been debated for many years. Mechanisms of demethylation within this organelle have also been postulated, but the exact mechanisms and their outcomes is still an active area of research. Mitochondrial dysfunction in the form of altered gene expression and ATP production, resulting from epigenetic changes, can lead to various conditions including aging-related neurodegenerative disorders, altered metabolism, changes in circadian rhythm, and cancer. Here, we provide an overview of the epigenetic regulation of mtDNA via methylation, long and short noncoding RNAs, and post-translational modifications of nucleoid proteins (as mitochondria lack histones). We also highlight the influence of xenobiotics such as airborne environmental pollutants, contamination from heavy metals, and therapeutic drugs on mtDNA methylation. Environ. Mol. Mutagen., 60:668-682, 2019. © 2019 Wiley Periodicals, Inc.

Mitochondrial transcription in mammalian cells

As a consequence of recent discoveries of intimate involvement of mitochondria with key cellular processes, there has been a resurgence of interest in all aspects of mitochondrial biology, including the intricate mechanisms of mitochondrial DNA maintenance and expression. Despite four decades of research, there remains a lot to be learned about the processes that enable transcription of genetic information from mitochondrial DNA to RNA, as well as their regulation. These processes are vitally important, as evidenced by the lethality of inactivating the central components of mitochondrial transcription machinery. Here, we review the current understanding of mitochondrial transcription and its regulation in mammalian cells. We also discuss key theories in the field and highlight controversial subjects and future directions as we see them.

Abnormally activated one-carbon metabolic pathway is associated with mtDNA hypermethylation and mitochondrial malfunction in the oocytes of polycystic gilt ovaries

Polycystic ovarian syndrome (PCOS) is associated with hyperhomocysteinemia and polycystic ovaries (PCO) usually produce oocytes of poor quality. However, the intracellular mechanism linking hyperhomocysteinemia and oocyte quality remains elusive. In this study, the quality of the oocytes isolated from healthy and polycystic gilt ovaries was evaluated in vitro in association with one-carbon metabolism, mitochondrial DNA (mtDNA) methylation, and mitochondrial function. PCO oocytes demonstrated impaired polar body extrusion, and significantly decreased cleavage and blastocyst rates. The mitochondrial distribution was disrupted in PCO oocytes, together with decreased mitochondrial membrane potential and deformed mitochondrial structure. The mtDNA copy number and the expression of mtDNA-encoded genes were significantly lower in PCO oocytes. Homocysteine concentration in follicular fluid was significantly higher in PCO group, which was associated with significantly up-regulated one-carbon metabolic enzymes betaine homocysteine methyltransferase (BHMT), glycine N-methyltransferase (GNMT) and the DNA methyltransferase DNMT1. Moreover, mtDNA sequences coding for 12S, 16S rRNA and ND4, as well as the D-loop region were significantly hypermethylated in PCO oocytes. These results indicate that an abnormal activation of one-carbon metabolism and hypermethylation of mtDNA may contribute, largely, to the mitochondrial malfunction and decreased quality of PCO-derived oocytes in gilts.

Transcriptional origin of Euglena chloroplast tRNAs

tRNA.DNA hybridization studies indicate that Euglena chloroplast tRNAs are transcriptional products of the chloroplast genome, which contains approximately 26 tRNA cistrons. Hybridization with purified chloroplast tRNA(Phe) and tRNA(Asp) shows that the chloroplast genome contains one cistron for each of these two species. No hybridization of chloroplast tRNA with nuclear DNA was observed. tRNAs from Euglena cytoplasm, Escherichia coli, and Agmenellum quadraduplicatum do not compete with chloroplast tRNA for hybridization with chloroplast DNA. Evidence is presented that photoinduction of chloroplast tRNAs is at the level of transcription rather than maturation of tRNA precursor molecules.

Synthesis and turnover of mitochondrial ribonucleic acid in HeLa cells: the mature ribosomal and messenger ribonucleic acid species are metabolically unstable

The synthesis rates and half-lives of the individual mitochondrial ribosomal ribonucleic acid (RNA) and polyadenylic acid-containing RNA species in HeLa cells have been determined by analyzing their kinetics of labeling with [5-3H]-uridine and the changes in specific activity of the mitochondrial nucleotide precursor pools. In one experiment, a novel method for determining the nucleotide precursor pool specific activities, using nascent RNA chains, has been utilized. All mitochondrial RNA species analyzed were found to be metabolically unstable, with half-lives of 2.5 to 3.5 h for the two ribosomal RNA components and between 25 and 90 min for the various putative messenger RNAs. A cordycepin "chase" experiment yielded half-life values for the messenger RNA species which were, in general, larger by a factor of 1.5 to 2.5 than those estimated in the labeling kinetics experiments. On the basis of previous observations, a model is proposed whereby the rate of mitochondrial RNA decay is under feedback control by some mechanism linked to RNA synthesis or processing. A short half-life was determined for five large polyadenylated RNAs, which are probably precursors of mature species. A rate of synthesis of one to two molecules per minute per cell was estimated for the various H-strand-coded messenger RNA species, and a rate of synthesis 50 to 100 times higher was estimated for the ribosomal RNA species. These data indicate that the major portion of the H-strand in each mitochondrial deoxyribonucleic acid molecule is transcribed very infrequently, possibly as rarely as once or twice per cell generation. Furthermore, these results are consistent with a previously proposed model of H-strand transcription in the form of a single polycistronic molecule.

Molecular cloning of cDNA for human von Willebrand factor: authentication by a new method

We have identified a 2.4 kb partial cDNA clone (pDL34) for human von Willebrand factor (vWf) mRNA. pDL34 was selected by screening an endothelial cell cDNA library with a radiolabeled reverse transcript of mRNA obtained by specific immunoisolation of vWf polysomes from endothelial cells. pDL34 selectively hybridized to an endothelial cell-associated 9.5 kb mRNA. To confirm its identity, SP6 RNA polymerase was used to generate in vitro transcripts of the cDNA. This synthetic RNA, truncated at its 5' end, directed the synthesis of several unique polypeptides in rabbit reticulocyte lysates. These polypeptides were immunoprecipitated by polyclonal and monoclonal anti-vWf antibodies. These results indicate that pDL34 contains an authentic partial copy of vWf mRNA. In vitro transcription of partial cDNA clones and translation of the resulting RNAs may be a useful general method of verifying the identity of various cDNA clones in circumstances where antibodies are available and protein sequence is not.

Nucleotide sequences of small ribosomal RNA and adjacent transfer RNA genes in rat mitochondrial DNA

The nucleotide sequences of genes for small 12 S ribosomal RNA and two transfer RNAs (tRNAPhe and tRNAVal) and their common upstream region in cloned rat mitochondrial DNA were determined. This DNA sequence of 1709 bp extends between the HindII and HindIII cleavage sites in the EcoRI-A and EcoRI-D fragments, respectively. There is no long reading frame for protein synthesis starting from the HindIII site and extending all the way to the HindII site, or vice versa. The heavy strand was found to be the template for these RNA transcripts. The 5' and 3' ends of the 12 S ribosomal RNA gene are contiguous with the tRNAPhe and tRNAVal genes, respectively. The structural features of the two tRNA genes are significantly different from the standard prokaryotic tRNA pattern. Since similar contiguous natures of these genes in human (Crews and Attardi, Cell 19 (1980) 775; Eperon et al., Nature 286 (1980) 460) and mouse (Van Etten et al., Cell 22 (1980) 157) mitochondrial DNA have been reported, comparative studies on the structures of these genes were performed by computer analysis and the characteristic features are discussed.

Synthesis and turnover of mitochondrial ribonucleic acid in HeLa cells: the mature ribosomal and messenger ribonucleic acid species are metabolically unstable

The synthesis rates and half-lives of the individual mitochondrial ribosomal ribonucleic acid (RNA) and polyadenylic acid-containing RNA species in HeLa cells have been determined by analyzing their kinetics of labeling with [5-3H]-uridine and the changes in specific activity of the mitochondrial nucleotide precursor pools. In one experiment, a novel method for determining the nucleotide precursor pool specific activities, using nascent RNA chains, has been utilized. All mitochondrial RNA species analyzed were found to be metabolically unstable, with half-lives of 2.5 to 3.5 h for the two ribosomal RNA components and between 25 and 90 min for the various putative messenger RNAs. A cordycepin "chase" experiment yielded half-life values for the messenger RNA species which were, in general, larger by a factor of 1.5 to 2.5 than those estimated in the labeling kinetics experiments. On the basis of previous observations, a model is proposed whereby the rate of mitochondrial RNA decay is under feedback control by some mechanism linked to RNA synthesis or processing. A short half-life was determined for five large polyadenylated RNAs, which are probably precursors of mature species. A rate of synthesis of one to two molecules per minute per cell was estimated for the various H-strand-coded messenger RNA species, and a rate of synthesis 50 to 100 times higher was estimated for the ribosomal RNA species. These data indicate that the major portion of the H-strand in each mitochondrial deoxyribonucleic acid molecule is transcribed very infrequently, possibly as rarely as once or twice per cell generation. Furthermore, these results are consistent with a previously proposed model of H-strand transcription in the form of a single polycistronic molecule.

The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA

A detailed transcription map of HeLa cell mitochondrial DNA (mtDNA) has been constructed by using the S1 protection technique to localize precisely the sequences coding for the ribosomal RNA (rRNA) and poly(A)-containing species on the physical map of the DNA. This transcription map has been correlated with the positions of the tRNA genes derived from the mtDNA sequence. It has been shown that, with the exception of the D loop and another small segment near the origin of replication, the mtDNA sequences are completely saturated by the rRNAs, poly(A)-containing RNAs and tRNA coded for by the two strands. No evidence for intervening sequences has been found. The sequences coding for the individual poly(A)-containing RNA and rRNA species appear to be immediately contiguous on one side, and most frequently on both sides, to tRNA coding sequences. Furthermore, the H strand sequences coding for the two rRNAs, the poly(A)-containing RNAs and the tRNAs appear to be adjacent to each other, extending from coordinate 2/100 to coordinate 95/100 of the genome relative to the origin taken as 0/100. The results are consistent with a model of transcription of the H strand in the form of a single molecule which is processed into mature RNA species by precise endonucleolytic cleavages, occurring in almost all cases immediately before and after a tRNA sequence. The tRNA sequences may play an important role as recognition signals in the processing of the primary transcripts.

Distinctive sequence of human mitochondrial ribosomal RNA genes

The nucleotide sequence spanning the ribosomal RNA (rRNA) genes of cloned human mitochondrial DNA reveals an extremely compact genome organization wherein the putative tRNA genes are probably 'butt-jointed' around the two rRNA genes. The sequences of the rRNA genes are significantly homologous in some regions to eukaryotic and prokaryotic sequences, but distinctive; the tRNA genes also have unusual nucleotide sequences. It seems that human mitochondria did not originate from recognizable relatives of present day organisms.

Mapping of nascent light and heavy strand transcripts on the physical map of HeLa cell mitochondrial DNA

The sequences complementary to the nascent RNA molecules isolated from transcription complexes of HeLa cell mtDNA have been mapped on the H and L strands of mtDNA by the S1 protection technique. The distribution of these sequences among different Hpa II restriction fragments was found to reflect the position of these fragments in the Hpa II map of mtDNA. Thus, the S1-resistant hybrids formed with the L strand corresponded almost exclusively to the right half of the genome past the origin of replication in the direction of L strand transcription, and were especially concentrated in the region immediately adjacent to the origin. By contrast, the hybrid duplexes involving the H strand appeared to be localized in the left half of the genome, and in particular in the quadrant of the map adjacent to the origin in the direction of H strand transcription. These results strongly suggest that the region of mtDNA around the origin of replication contains an initiation site for L strand transcription and an initiation site for H strand transcription.

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.

Chemical and physical properties of mammalian mitochondrial aminoacyl-transfer RNAs. I. Molecular weights of mitochondrial leucyl- and methionyl-transfer RNAs

The sedimentation and electrophoretic properties of Syrian hamster cytosolix and mitochondrial methionyl- and leucyl- +RNAs have been compared under denaturing conditions. Mitochondrial leucyl-tRNA could be separated into three species by chromatography on RPC-5. Their apparent molecule weights as determined by polyacrylamide slab gel elecltrophoresis were 23 000 for one species and 24 000 for the other two compared to the five cytosolic leucyl-tRNA species whose apparent molecular weights ranged from 26 000 to 28 000. Mitochondrial leucyl-tRNAs sedimented more slowly than their cytosolic counterparts, again indicating a lower molecular weight. The apparent molecular weights of the mitochondrial methionyl-tRNAs were identical or only slightly lower than their cytosolic counterparts as determined by polyacrylamide slab gel electrophoresis but both mitochondrial methionyl-tRNA and formylmethionyl-tRNA sedimented slightly more slowly than cytolsolic methionyl-tRNA. It is suggested that mitochondrial tRNAs fall into the size range of other t RNAs and might be uniform in size.

Polyribosomes and messenger RNA from rat liver mitochondria

Rat liver mitochondrial polyribosomes were isolated free from cytoplasmic ribonucleoprotein contaminations in a number of criteria (sedimentation and buoyant density patterns, ribosomal RNA composition). Heterogeneous poly A containing RNA from mitochondrial polysomes was purified by two-stage cellulose chromatography. This RNA was in vitro labelled with 125I up to specific activity approximately 10(6)-10(7) cts.min-1.microng-1 and used for hybridization experiments with separate complementary strands of mitochondrial DNA and nuclear DNA fragments. The proportions of mitochondrial poly A containing RNA that is complementary to heavy and light strands of mtDNA were respectively 31.5% and 8.3%. Besides, a significant RNA fraction was complementary to unique sequences of nuclear DNA (2-3 copies per haploid genome). The hybrids that were formed possessed a high Tm indicative of a perfect base pairing. A dual intracellular origin of mitochondrial messenger RNA is discussed.

Molecular and genetic approaches to the analysis of the informational content of the mitochondrial genome in mammalian cells

Our laboratory has been involved in the last few years in investigations aiming at analysing by molecular approaches the informational content of the mitochondrial genome in mammalian cells and the mechanisms and control of its expression, H eLa cells and other mammalian cell lines have been utilized for these studies. These investigations, as well as work carried out in other laboratories, have yielded a considerable amount of information concerning the mechanism, products and regulation of transcription of mitochondrial DNA (mit-DNA), the apparatus and products of mitochondria-specific protein synthesis in animal cells, and the number and topology of the sites on mit-DNA which code for the primary gene products identified so far. It is the purpose of the present report to summarize the latest observations in this area, as well as some recent results on the isolation and characterization of chloramphenicol-resistant variants of a human cell line. Reference is made to previous review articles 1,2,3 for the earlier work.

An electron microscope study of the relative positions of the 4S and ribosomal RNA genes in HeLa cells mitochondrial DNA

The 4S RNA genes in HeLa mitochondrial DNA (mtDNA) have been mapped by electron microscopy using the electron-opaque label ferritin. This method is based on the high affinity interaction between the protein, avidin,and biotin. 4S RNA, covalently coupled to biotin, was hybridized to single-stranded mtDNA. The hybrids were then labeled with ferritin-avidin conjugates. The positions of ferritin-labeled 4S RNA genes were determined relative to the rRNA genes on both heavy (H) and light (L) strands of mtDNA. This region was recognized as a duplex segment after hybridization either with rRNA in the case of H strands or with DNA complementary to rRNA in the case of L strands. Our studies suggest that at least nineteen 4S RNA genes are present in the HeLa mitochondrial genome. On the H strand, we have confirmed the nine map positions found in a previous electron microscope mapping study (Wu et al., 1972) and obtained evidence for three additional 4S RNA genes. On the L strand, seven 4S RNA genes have been mapped. The nineteen genes are distributed more or less uniformly around the genome. There is a pair of closely spaced genes, approximately 150 nucleotides apart, on the H strand, and another closely spaced pair on the L strand.

Hybridization of mitochondrial and cytoplasmic ribosomal RNA with mitochondrial and nuclear DNA

Hybridization assays of rat liver mitochondrial and cytoplasmic rRNAs with in vitro labelled mitochondrial and nuclear DNA were performed in liquid medium. Sensitivity towards S1 enzyme and Tms of the RNA-DNA hybrids were studied. Our results are in favour of a distinct genetic origin of the two types of cellular rRNAs.

Heterogeneity of mitochondrial DNA from Saccharomyces cerevisiae and genetic information for tRNA

Mitochondrial DNA from wild-type Saccharomyces cerevisiae and from an "extreme" petite mutant were analyzed by hybridization of several tRNAs on DNA fragments of different buoyant density, obtained by sonication and fractionation on a CsCl gradient. The hybridization patterns show that the genes for tRNAser, tRNAphe, tRNAhis, tRNAval, tRNAileu are present on wild-type mitochondrial DNA, while only genes for tRNAser and tRNAhis are present on petite mitochondrial DNA; moreover the hybridization patterns indicate that these genes are not clustered and suggest that more than one gene might exist for tRNAser and tRNAhis.

Cytoplasmic transfer of chloramphenicol resistance in human tissue culture cells

The cytoplasmic inheritance of human chloramphenicol (cap) resistance has been demonstrated by removing the nuclei of cells of the CAP-resistant HeLa strain 296-1 (enucleation) and fusing them to a CAP-sensitive HeLa strain lacking nuclear thymidine kinase. Plating the fusion products in bromodeoxyuridine and CAP resulted in the growth of about 150 colonies/10(6) parent cells plated. Permanent cell lines (cybrids) grown from such fusions have been designated HEB. A recloned HEB cybrid (HEB7A) has also been enucleated and fused to hypoxanthine phosphoribosyl transferase (HPRT)-deficient HeLa cells (S3AG1) and HPRT-deficient lymphocytes (WAL-2A). Cybrids were selected in thioguanine and CAP. In the fusion of enucleated (en) HEB7A to S3AG1, 1,200 colonies/10(6) parents were observed. Fusion of enHEB7A to WAL-2A was done in mass culture and cybrids were obtained on three separate occasions. In every case the parental controls were negative. All isolates tested from the above fusions have the CAP-resistant characteristics, in vivo and in vitro, of the enucleated parent and the nuclear characteristics of the CAP-sensitive parent, such as chromosome number, morphology, and specific isozyme and chromosome markers. Therefore, it can be concluded that CAP resistance is coded in the cytoplasm and not in the nucleus of 296-1 cells. Furthermore, this resistance can be transferred to cells of widely different origin and differentiated state. These studies represent the first genetic evidence of cytoplasmic inheritance in human cells.

Number of genes and base composition of mitochondrial tRNA from Saccharomyces cerevisiae

Increasing amounts of mitochondrial [32P] tRNA (4S fraction), were hybridized with mitochondrial DNA OF Saccharomyces cerevisiae. At saturation, the calculated number of genes for 4S mitochondrial RNA was 20. Mitochondrial [32P] tRNA eluted from the hydrids obtained either with an excess of tRNA or an excess of DNA showed, after alkaline hydrolysis and chromatography, a G+C content of 28 and 35 p. cent respectively. This last value is similar to that found with the total 4S fraction. The odd nucleotides T (about 1T per sequence), U, hU are present in mitochondrial tRNA. Some sequence may begin with pG.

Identification of discrete polyadenylate-containing RNA components transcribed from HeLa cell mitochondrial DNA

Polyacrylamide gel electrophoresis and sedimentation analysis under denaturing conditions of poly(A)-containing RNA from the polysome region of the sedimentation pattern of a HeLa-cell mitochondrial lysate has revealed the occurrence of a discrete RNA component, which sediments in the native state with a sedimentation constant of about 7 S. From the sedimentation behavior under native and denaturing conditions and the poly(A) content, a molecular weight of about 9 x 10(4) has been estimated for this component. RNA.DNA hybridization experiments have indicated that this component is coded for by the light strand of mitochondrial DNA. Evidence for the occurrence of a poly(A)-containing RNA component sedimenting at about 9 S and coded for by the heavy strand has also been obtained.

Atypical pattern of utilization of amino acids for mitochondrial protein synthesis in HeLa cells

The capacity of HeLa cell mitochondria, either isolated or in intact cells, to incorporate different labeled amino acids into proteins was investigated. Eight amino acids (alanine, arginine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, and lysine), which include most of the charged polar ones, showed a very low amount, if any at all, of chloramphenicol-sensitive incorporation, relative to that expected for an "average" HeLa-cell protein. By contrast, the most hydrophobic amino acids (leucine, isoleucine, valine, phenylalanine, and methionine) were the most actively incorporated by HeLa mitochondria. The available evidence suggests that pool effects cannot account for this general pattern of utilization of amino acids; furthermore, this pattern is in good agreement with the known hydrophobic properties of proteins synthesized in mitochondria.