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The functional organization of mitochondrial genomes in human cells.

Iborra FJ, Kimura H, Cook PR - BMC Biol. (2004)

Bottom Line: This mitochondrial RNA colocalizes with components of the cytoplasmic machinery that makes and imports nuclear-encoded proteins - that is, a ribosomal protein (S6), a nascent peptide associated protein (NAC), and the translocase in the outer membrane (Tom22).The results suggest that clusters of mitochondrial genomes organize the translation machineries on both sides of the mitochondrial membranes.Then, proteins encoded by the nuclear genome and destined for the mitochondria will be made close to mitochondrial-encoded proteins so that they can be assembled efficiently into mitochondrial complexes.

View Article: PubMed Central - HTML - PubMed

Affiliation: MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, OX3 9DS, UK. francisco.iborra@imm.ox.ac.uk <francisco.iborra@imm.ox.ac.uk>

ABSTRACT

Background: We analyzed the organization and function of mitochondrial DNA in a stable human cell line (ECV304, which is also known as T-24) containing mitochondria tagged with the yellow fluorescent protein.

Results: Mitochondrial DNA is organized in approximately 475 discrete foci containing 6-10 genomes. These foci (nucleoids) are tethered directly or indirectly through mitochondrial membranes to kinesin, marked by KIF5B, and microtubules in the surrounding cytoplasm. In living cells, foci have an apparent diffusion constant of 1.1 x 10(-3) microm2/s, and mitochondria always split next to a focus to distribute all DNA to one daughter. The kinetics of replication and transcription (monitored by immunolabelling after incorporating bromodeoxyuridine or bromouridine) reveal that each genome replicates independently of others in a focus, and that newly-made RNA remains in a focus (residence half-time approximately 43 min) long after it has been made. This mitochondrial RNA colocalizes with components of the cytoplasmic machinery that makes and imports nuclear-encoded proteins - that is, a ribosomal protein (S6), a nascent peptide associated protein (NAC), and the translocase in the outer membrane (Tom22).

Conclusions: The results suggest that clusters of mitochondrial genomes organize the translation machineries on both sides of the mitochondrial membranes. Then, proteins encoded by the nuclear genome and destined for the mitochondria will be made close to mitochondrial-encoded proteins so that they can be assembled efficiently into mitochondrial complexes.

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Mitochondrial replication. Cells with YFP-tagged mitochondria were grown in BrdU for 1–6 h, fixed, and Br-DNA immunolabelled. (A,B) On growth in BrdU, progressively more mitochondrial foci containing Br-DNA are seen. Bar: 2 μm. (C) Changes in the fraction of DNA foci containing Br-DNA (assuming cells contain 468 foci/cell; Table 1, line 3); essentially all foci contain Br-DNA within 3 h. (D) Integrated intensity of Br-DNA labelling per focus (in arbitrary units, with the value at 1 h set to unity). The average intensity per focus is constant between 1 and 2 h, and then rises; extrapolating the line from 2–6 h to 22 h (the length of the cell cycle) gives an intensity of 10 (square). (E) Three models for replication. Two DNA foci, each initially containing 10 unreplicated genomes (open circles), are shown. (a) Here, a focus is a unit of replication. In the first hour, all genomes in one focus replicate together (red circles) and half the foci become labelled (as in Figure 6C); in the second hour, all genomes in a second focus replicate together so that all genomes are now labelled (again as in Figure 6C). However, during the third hour, the intensity of foci continues to increase (Figure 6D), so we would have to assume that genomes re-replicate (dark red circles) and some would presumably have to be degraded to maintain genome numbers. (b) All genomes replicate independently of all others. The kinetics in (D) and (E) are consistent with this model. (c) Here, a polymerizing complex transfers from genome to genome in one focus before going to another focus; then genomes in one focus would replicate successively, before replication switched to another focus. This would give the progressive increase seen in Figure 6D, but many foci would remain unlabelled after 2 h (which is inconsistent with Figure 6E).
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Figure 6: Mitochondrial replication. Cells with YFP-tagged mitochondria were grown in BrdU for 1–6 h, fixed, and Br-DNA immunolabelled. (A,B) On growth in BrdU, progressively more mitochondrial foci containing Br-DNA are seen. Bar: 2 μm. (C) Changes in the fraction of DNA foci containing Br-DNA (assuming cells contain 468 foci/cell; Table 1, line 3); essentially all foci contain Br-DNA within 3 h. (D) Integrated intensity of Br-DNA labelling per focus (in arbitrary units, with the value at 1 h set to unity). The average intensity per focus is constant between 1 and 2 h, and then rises; extrapolating the line from 2–6 h to 22 h (the length of the cell cycle) gives an intensity of 10 (square). (E) Three models for replication. Two DNA foci, each initially containing 10 unreplicated genomes (open circles), are shown. (a) Here, a focus is a unit of replication. In the first hour, all genomes in one focus replicate together (red circles) and half the foci become labelled (as in Figure 6C); in the second hour, all genomes in a second focus replicate together so that all genomes are now labelled (again as in Figure 6C). However, during the third hour, the intensity of foci continues to increase (Figure 6D), so we would have to assume that genomes re-replicate (dark red circles) and some would presumably have to be degraded to maintain genome numbers. (b) All genomes replicate independently of all others. The kinetics in (D) and (E) are consistent with this model. (c) Here, a polymerizing complex transfers from genome to genome in one focus before going to another focus; then genomes in one focus would replicate successively, before replication switched to another focus. This would give the progressive increase seen in Figure 6D, but many foci would remain unlabelled after 2 h (which is inconsistent with Figure 6E).

Mentions: In mouse L cells, individual mtDNA molecules are selected randomly for replication throughout the cell cycle [32]. Active sites of synthesis can be localized after growing cells in BrdU, and then immunolabelling the resulting Br-DNA; Davis and Clayton [36] found that perinuclear mitochondria appear to be more synthetically active than peripheral ones. However, when we repeated this experiment, we found mitochondria in different regions were equally active, although the perinuclear region contained a higher concentration of mitochondria (Figure 6A,6B,6C). A similar result to ours has been obtained recently by Magnusson et al. [37]. The differences seen could arise from intrinsic differences between the cell types studied, or from an improved detection of Br-DNA at the periphery (where there are fewer mitochondria). The number of labelled foci increased on growth in BrdU for 3 h and then remained constant (Figure 6C); conversely, the average intensity per focus initially remained constant for 2 h and then increased (Figure 6D).


The functional organization of mitochondrial genomes in human cells.

Iborra FJ, Kimura H, Cook PR - BMC Biol. (2004)

Mitochondrial replication. Cells with YFP-tagged mitochondria were grown in BrdU for 1–6 h, fixed, and Br-DNA immunolabelled. (A,B) On growth in BrdU, progressively more mitochondrial foci containing Br-DNA are seen. Bar: 2 μm. (C) Changes in the fraction of DNA foci containing Br-DNA (assuming cells contain 468 foci/cell; Table 1, line 3); essentially all foci contain Br-DNA within 3 h. (D) Integrated intensity of Br-DNA labelling per focus (in arbitrary units, with the value at 1 h set to unity). The average intensity per focus is constant between 1 and 2 h, and then rises; extrapolating the line from 2–6 h to 22 h (the length of the cell cycle) gives an intensity of 10 (square). (E) Three models for replication. Two DNA foci, each initially containing 10 unreplicated genomes (open circles), are shown. (a) Here, a focus is a unit of replication. In the first hour, all genomes in one focus replicate together (red circles) and half the foci become labelled (as in Figure 6C); in the second hour, all genomes in a second focus replicate together so that all genomes are now labelled (again as in Figure 6C). However, during the third hour, the intensity of foci continues to increase (Figure 6D), so we would have to assume that genomes re-replicate (dark red circles) and some would presumably have to be degraded to maintain genome numbers. (b) All genomes replicate independently of all others. The kinetics in (D) and (E) are consistent with this model. (c) Here, a polymerizing complex transfers from genome to genome in one focus before going to another focus; then genomes in one focus would replicate successively, before replication switched to another focus. This would give the progressive increase seen in Figure 6D, but many foci would remain unlabelled after 2 h (which is inconsistent with Figure 6E).
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Figure 6: Mitochondrial replication. Cells with YFP-tagged mitochondria were grown in BrdU for 1–6 h, fixed, and Br-DNA immunolabelled. (A,B) On growth in BrdU, progressively more mitochondrial foci containing Br-DNA are seen. Bar: 2 μm. (C) Changes in the fraction of DNA foci containing Br-DNA (assuming cells contain 468 foci/cell; Table 1, line 3); essentially all foci contain Br-DNA within 3 h. (D) Integrated intensity of Br-DNA labelling per focus (in arbitrary units, with the value at 1 h set to unity). The average intensity per focus is constant between 1 and 2 h, and then rises; extrapolating the line from 2–6 h to 22 h (the length of the cell cycle) gives an intensity of 10 (square). (E) Three models for replication. Two DNA foci, each initially containing 10 unreplicated genomes (open circles), are shown. (a) Here, a focus is a unit of replication. In the first hour, all genomes in one focus replicate together (red circles) and half the foci become labelled (as in Figure 6C); in the second hour, all genomes in a second focus replicate together so that all genomes are now labelled (again as in Figure 6C). However, during the third hour, the intensity of foci continues to increase (Figure 6D), so we would have to assume that genomes re-replicate (dark red circles) and some would presumably have to be degraded to maintain genome numbers. (b) All genomes replicate independently of all others. The kinetics in (D) and (E) are consistent with this model. (c) Here, a polymerizing complex transfers from genome to genome in one focus before going to another focus; then genomes in one focus would replicate successively, before replication switched to another focus. This would give the progressive increase seen in Figure 6D, but many foci would remain unlabelled after 2 h (which is inconsistent with Figure 6E).
Mentions: In mouse L cells, individual mtDNA molecules are selected randomly for replication throughout the cell cycle [32]. Active sites of synthesis can be localized after growing cells in BrdU, and then immunolabelling the resulting Br-DNA; Davis and Clayton [36] found that perinuclear mitochondria appear to be more synthetically active than peripheral ones. However, when we repeated this experiment, we found mitochondria in different regions were equally active, although the perinuclear region contained a higher concentration of mitochondria (Figure 6A,6B,6C). A similar result to ours has been obtained recently by Magnusson et al. [37]. The differences seen could arise from intrinsic differences between the cell types studied, or from an improved detection of Br-DNA at the periphery (where there are fewer mitochondria). The number of labelled foci increased on growth in BrdU for 3 h and then remained constant (Figure 6C); conversely, the average intensity per focus initially remained constant for 2 h and then increased (Figure 6D).

Bottom Line: This mitochondrial RNA colocalizes with components of the cytoplasmic machinery that makes and imports nuclear-encoded proteins - that is, a ribosomal protein (S6), a nascent peptide associated protein (NAC), and the translocase in the outer membrane (Tom22).The results suggest that clusters of mitochondrial genomes organize the translation machineries on both sides of the mitochondrial membranes.Then, proteins encoded by the nuclear genome and destined for the mitochondria will be made close to mitochondrial-encoded proteins so that they can be assembled efficiently into mitochondrial complexes.

View Article: PubMed Central - HTML - PubMed

Affiliation: MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, OX3 9DS, UK. francisco.iborra@imm.ox.ac.uk <francisco.iborra@imm.ox.ac.uk>

ABSTRACT

Background: We analyzed the organization and function of mitochondrial DNA in a stable human cell line (ECV304, which is also known as T-24) containing mitochondria tagged with the yellow fluorescent protein.

Results: Mitochondrial DNA is organized in approximately 475 discrete foci containing 6-10 genomes. These foci (nucleoids) are tethered directly or indirectly through mitochondrial membranes to kinesin, marked by KIF5B, and microtubules in the surrounding cytoplasm. In living cells, foci have an apparent diffusion constant of 1.1 x 10(-3) microm2/s, and mitochondria always split next to a focus to distribute all DNA to one daughter. The kinetics of replication and transcription (monitored by immunolabelling after incorporating bromodeoxyuridine or bromouridine) reveal that each genome replicates independently of others in a focus, and that newly-made RNA remains in a focus (residence half-time approximately 43 min) long after it has been made. This mitochondrial RNA colocalizes with components of the cytoplasmic machinery that makes and imports nuclear-encoded proteins - that is, a ribosomal protein (S6), a nascent peptide associated protein (NAC), and the translocase in the outer membrane (Tom22).

Conclusions: The results suggest that clusters of mitochondrial genomes organize the translation machineries on both sides of the mitochondrial membranes. Then, proteins encoded by the nuclear genome and destined for the mitochondria will be made close to mitochondrial-encoded proteins so that they can be assembled efficiently into mitochondrial complexes.

Show MeSH