Individual Nucleoids Research Articles

Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA.

Cellular metabolism relies on the regulation and maintenance of mitochondrial DNA (mtDNA). Hundreds to thousands of copies of mtDNA exist in each cell, yet because mitochondria lack histones or other machinery important for nuclear genome compaction, it remains unresolved how mtDNA is packaged into individual nucleoids. In this study, we used long-read single-molecule accessibility mapping to measure the compaction of individual full-length mtDNA molecules at near single-nucleotide resolution. We found that, unlike the nuclear genome, human mtDNA largely undergoes all-or-none global compaction, with most nucleoids existing in an inaccessible, inactive state. Highly accessible mitochondrial nucleoids are co-occupied by transcription and replication components and selectively form a triple-stranded displacement loop structure. In addition, we showed that the primary nucleoid-associated protein TFAM directly modulates the fraction of inaccessible nucleoids both in vivo and in vitro, acting consistently with a nucleation-and-spreading mechanism to coat and compact mitochondrial nucleoids. Together, these findings reveal the primary architecture of mtDNA packaging and regulation in human cells.

The TFAM-to-mtDNA ratio defines inner-cellular nucleoid populations with distinct activity levels.

In human cells, generally a single mitochondrial DNA (mtDNA) is compacted into a nucleoprotein complex denoted the nucleoid. Each cell contains hundreds of nucleoids, which tend to cluster into small groups. It is unknown whether all nucleoids are equally involved in mtDNA replication and transcription or whether distinct nucleoid subpopulations exist. Here, we use multi-color STED super-resolution microscopy to determine the activity of individual nucleoids in primary human cells. We demonstrate that only a minority of all nucleoids are active. Active nucleoids are physically larger and tend to be involved in both replication and transcription. Inactivity correlates with a high ratio of the mitochondrial transcription factor A (TFAM) to the mtDNA of the individual nucleoid, suggesting that TFAM-induced nucleoid compaction regulates nucleoid replication and transcription activity invivo. We propose that the stable population of highly compacted inactive nucleoids represents a storage pool of mtDNAs with a lower mutational load.

Chloroplast nucleoids are highly dynamic in ploidy, number, and structure during angiosperm leaf development.

Chloroplast nucleoids are large, compact nucleoprotein structures containing multiple copies of the plastid genome. Studies on structural and quantitative changes of plastid DNA (ptDNA) during leaf development are scarce and have produced controversial data. We have systematically investigated nucleoid dynamics and ptDNA quantities in the mesophyll of Arabidopsis, tobacco, sugar beet, and maize from the early post-meristematic stage until necrosis. DNA of individual nucleoids was quantified by DAPI-based supersensitive epifluorescence microscopy. Nucleoids occurred in scattered, stacked, or ring-shaped arrangements and in recurring patterns during leaf development that was remarkably similar between the species studied. Nucleoids per organelle varied from a few in meristematic plastids to >30 in mature chloroplasts (corresponding to about 20-750 nucleoids per cell). Nucleoid ploidies ranged from haploid to >20-fold even within individual organelles, with average values between 2.6-fold and 6.7-fold and little changes during leaf development. DNA quantities per organelle increased gradually from about a dozen plastome copies in tiny plastids of apex cells to 70-130 copies in chloroplasts of about 7μm diameter in mature mesophyll tissue, and from about 80 plastome copies in meristematic cells to 2600-3300 copies in mature diploid mesophyll cells without conspicuous decline during leaf development. Pulsed-field electrophoresis, restriction of high-molecular-weight DNA from chloroplasts and gerontoplasts, and CsCl equilibrium centrifugation of single-stranded and double-stranded ptDNA revealed no noticeable fragmentation of the organelle DNA during leaf development, implying that plastid genomes in mesophyll tissues are remarkably stable until senescence.

Underlying regularity in the shapes of nucleoids of Escherichia coli: Implications for nucleoid organization and partition

The genomic DNA of Escherichia coli is localized in one or a few compact nucleoids. Nucleoids in rapidly grown cells appear in complex shapes; the relationship of these shapes to underlying arrangements of the DNA is of structural interest and of potential importance in gene localization and nucleoid partition studies. To help assess this variation in shape, limited three-dimensional information on individual nucleoids was obtained by DNA fluorescence microscopy of cells as they reoriented in solution or by optical sectioning. These techniques were also applied to enlarged nucleoids within swollen cells or spheroplasts. The resulting images indicated that much of the apparent variation was due to imaging from different directions and at different focal planes of more regular underlying nucleoid shapes. Nucleoid images could be transformed into compact doublet shapes by exposure of cells to chloramphenicol or puromycin, consistent with a preexisting bipartite nucleoid structure. Isolated nucleoids and nucleoids in stationary-phase cells also assumed a doublet shape, supporting such a structure. The underlying structure is suggested to be two subunits joined by a linker. Both the subunits and the linker appear to deform to accommodate the space available within cells or spheroplasts (“flexible doublet” model).

The numbers of individual mitochondrial DNA molecules and mitochondrial DNA nucleoids in yeast are co-regulated by the general amino acid control pathway.

Mitochondrial DNA (mtDNA) is inherited as a protein-DNA complex (the nucleoid). We show that activation of the general amino acid response pathway in rho(+) and rho(-) petite cells results in an increased number of nucleoids without an increase in mtDNA copy number. In rho(-) cells, activation of the general amino acid response pathway results in increased intramolecular recombination between tandemly repeated sequences of rho(-) mtDNA to produce small, circular oligomers that are packaged into individual nucleoids, resulting in an approximately 10-fold increase in nucleoid number. The parsing of mtDNA into nucleoids due to general amino acid control requires Ilv5p, a mitochondrial protein that also functions in branched chain amino acid biosynthesis, and one or more factors required for mtDNA recombination. Two additional proteins known to function in mtDNA recombination, Abf2p and Mgt1p, are also required for parsing mtDNA into a larger number of nucleoids, although expression of these proteins is not under general amino acid control. Increased nucleoid number leads to increased mtDNA transmission, suggesting a mechanism to enhance mtDNA inheritance under amino acid starvation conditions.

Delayed nucleoid segregation in Escherichia coli.

To study the role of cell division in the process of nucleoid segregation, we measured the DNA content of individual nucleoids in isogenic Escherichia coli cell division mutants by image cytometry. In pbpB(Ts) and ftsZ strains growing as filaments at 42 degrees C, nucleoids contained, on average, more than two chromosome equivalents compared with 1.6 in wild-type cells. Because similar results were obtained with a pbpB recA strain, the increased DNA content cannot be ascribed to the occurrence of chromosome dimers. From the determination of the amount of DNA per cell and per individual nucleoid after rifampicin inhibition, we estimated the C and D periods (duration of a round of replication and time between termination and cell division respectively), as well as the D' period (time between termination and nucleoid separation). Compared with the parent strain and in contrast to ftsQ, ftsA and ftsZ mutants, pbpB(Ts) cells growing at the permissive temperature (28 degrees C) showed a long D' period (42 min versus 18 min in the parent) indicative of an extended segregation time. The results indicate that a defective cell division protein such as PbpB not only affects the division process but also plays a role in the last stage of DNA segregation. We propose that PbpB is involved in the assembly of the divisome and that this structure enhances nucleoid segregation.

A correlation between nuclear supercoiling and the response of patients with bladder cancer to radiotherapy

Single cell tumour suspensions were prepared from biopsy and urine samples from 28 patients with muscle invasive transitional cell carcinoma of the bladder. Nuclear extracts (nucleoids) containing intact chromatin were isolated from these cells and the condensation of DNA supercoils measured by the light scattered from individual nucleoids within a flow cytometer. Exposure of these nucleoids to 10 micrograms ml-1 ethidium bromide produced 78.9% increase in light scatter compared to those treated with 50 micrograms ml-1. This finding is consistent with the known effect of ethidium bromide on DNA supercoiling and confirms that the light scatter signal is responding to changes at this level of DNA organisation. Cell samples were also exposed to 12 Gy of gamma radiation and the effect on nucleoid light scatter recorded. Of the patients studied prior to radiotherapy, those with persistent disease 3 months after treatment generated an increase in nucleoid light scatter of + 9.35 +/- 4.8% after 12 Gy irradiation, of these, 2/14 produced nucleoids that relaxed by more than 10% compared to controls. Those patients with no evidence of disease after radiotherapy gave an increase in nucleoid light scatter after in vitro irradiation of + 19.3 +/- 4.5% of which 10/14 (71%) relaxed by more than 10%. It is proposed that the increased relaxation within the supercoiled DNA from patients whose tumours were undetectable 3 months after therapy, is related to the inherent radiosensitivity of these tumour cells. Such a difference in nucleoid response within tumour cells from patients that responded to radiation may arise due to a decreased affinity of DNA loops for the nuclear matrix. This structural change, at a site associated with the initiation of DNA synthesis, may affect the ability of cells to continue successful cell division after radiation damage.

Changes in the number of chloroplast-nucleoids in the asexual reproduction cycle of [formula omitted

Changes in the number of chloroplast-nucleoids during the asexual reproduction cycle in the green alga, Hydrodictyon reticulatum were investigated with fluorochrome DAPI. The maximum number (50.3) was counted in immature zoospores, this value being about four times the minimum number (11.8) observed in the mature vegetative cell. The changes in the number of chlnucleoids per nucleus may possibly be due to aggregation between chl-nucleoids or separation into individual nucleoids. The total copy numbers of chloroplast genomes per nucleus appeared to be essentially constant at all stages.

DNA replication behaviour of individual nucleoids of two Streptomyces strains

AbstractDuring exponential growth mycelia of Streptomyces granaticolor and Streptomyces hygroscopicus were pulse‐labelled with 3H‐thymidine for different times. The distribution of silver grains was analyzed in the autoradiograms by using the unit cell‐concept, according to which a unit cell corresponds to the hyphal length containing one nucleoid, i. e. one genome equivalent.All nucleoids of the mycelia were labelled, if the pulse extended for more than 50% of the doubling time. Thus, in young mycelia there were no nucleoids in which had stopped replication at all. However, the mycelia showed an increasing fraction of non‐replicating nucleoids, if the pulse was shortened. This fact indicated that nucleoids transiently lacked replication.The fraction of non‐replicating nucleoids as determined from the latter samples allowed to calculate the replication time C of the individual nucleoids. The C period occupied about 54% of the doubling time in mycelia growing with a generation time of 96 to 415 min.Replication of neighboured nucleoids was not synchronous.

Early vegetative segregation of mitochondrial genes in Saccharomyces cerevisiae

The vegetative segregation of seven mitochondrial gene loci was studied in yeast. At various times after mating antibiotic resistant and sensitive strains, samples of the diploid progeny were examined to determine the segregation rates of the alleles at each locus in three- and four-factor crosses. The rate of segregation was approximately the same for the cap1, ery1, oli1, oli2, and par1 loci, which are scattered over about two-thirds of the mitochondrial DNA molecule. Differences in segregation rates were found but showed no consistent relationship to the map positions of the loci. This is in contrast to the segregation of chloroplast genes in Chlamydomonas, where loci segregate at rates proportional to their distance from an “attachment point” which appears to govern the partitioning of chloroplast DNA molecules between daughter chloroplasts when the chloroplast divides. Our data are compatible with a model in which the mitochondrial DNA molecules in a cell occur in a small number of groups corresponding to individual nucleoids or mitochondria. Most or all of the molecules in a group carry the same allele at any given locus. These genetically homogeneous groups of molecules may thus be the units of segregation, and may be partitioned randomly between mother cell and bud at each division.

Variable amounts of DNA related to the size of chloroplasts. IV. Three-dimensional arrangement of DNA in fully differentiated chloroplasts of Beta vulgaris L.

ABSTRACT Glutaraldehyde-fixed strips of fully differentiated leaves of Beta vulgaris L. were treated with proteases. With this method it is possible to display DNA-regions in chloroplasts selectively and to reconstruct them from serial sections. As in young plastids, the DNA in mature plastids is also distributed within several regions which are separated rather clearly by thylakoids. The number of such regions depends upon the size of the organelle and thus upon its developmental state. The shape of the regions is, in contrast to less-differentiated plastids, mostly elongated. The individual regions seem to contain unequal quantities of DNA-fibrils. A comparison of our ultrastructural results and biochemical data (DNA-amounts per plastid depending on the size of the organelle; kinetic complexity of chloroplast-DNA of Beta) as well as a comparison of the chloroplast with similar prokaryotic systems (as in bacteria, blue-green algae, and mitochondria) leads to the suggestion that each DNA-containing region can be regarded as a single nucleoid. In addition, each nucleoid already contains several (on average, 4–8) genetic units. Thus the chloroplast of Beta seems genetically polyvalent in at least 2 respects: (i) it is of polyenergidic organization, and (ii) the individual nucleoids can be polyploid to varying degrees.