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PubMed2001

Large amounts of apicoplast nucleoid DNA and its segregation in Toxoplasma gondii.

Apicoplasts (apicomplexan plastids) are nonphotosynthetic, secondary endosymbiotic plastids that are found in most apicomplexans. Although these organelles are essential for parasite survival, their functions, activities, and structures are not well understood. We examined the apicoplast nucleoid of Toxoplasma gondii from a morphological aspect by high-resolution epifluorescence microscopy and electron microscopy. We found unexpectedly large amounts of DNA in the nucleoid and the presence of several division-related structures. Initially, we identified the organellar nucleoids by staining with the DNA-specific dye 4',6-diamidino-2-phenylindole. A single nucleoid was observed per apicoplast, and the fluorescent spot representing the nucleoid was bright and spherical in contrast to the weak and filamentous spot representing the mitochondrial nucleoid. We also measured the DNA content of each apicoplast nucleoid by a video-intensified microscope photon-counting system and determined that the genomic copy number was at least 25, a figure over four times greater than that reported previously. Moreover, several groups of apicoplasts had significantly higher genomic copy numbers. The DNA molecules were accurately divided into two daughter apicoplasts just before nuclear division. In addition, we examined nucleoid segregation and the division apparatus using electron microscopy. However, we failed to observe nucleoid structures, suggesting that the apicoplasts are predominantly composed of nucleoid material. In addition, we observed "cap" structures at the termini of dividing apicoplasts, a possible plastid-dividing ring, and a microbody-like granule around the constriction. These structures may be involved in apicoplast division.

Animals↗

PubMed2002

Identification of the YMN-1 antigen protein and biochemical analyses of protein components in the mitochondrial nucleoid fraction of the yeast Saccharomyces cerevisiae.

We analyzed the protein components contained in the mitochondrial nucleoid (mt-nucleoid) fraction of the yeast Saccharomyces cerevisiae. Immunoblotting with anti-Abf2p antibody demonstrated the association of Abf2p, a major mitochondrial DNA-binding protein, with the mt-nucleoids. In contrast, porin and cytochrome c oxidase subunit III (CoxIIIp) were not detected by immunoblotting in the mt-nucleoid fraction. The YMN-1 monoclonal antibody recognized a 48 kDa protein of the mt-nucleoid fraction. The N-terminal amino acid sequence of the protein and immunological evidence showed that the YMN-1 monoclonal antibody recognizes dihydrolipoyl transsuccinylase (KE2), which is one of the constituents of the alpha-ketoglutarate dehydrogenase complex (KGDC). alpha-Ketoglutarate dehydrogenase (KE1) and dihydrolipoyl dehydrogenase (E3), which are other subunits of KGDC, were also detected in the mt-nucleoid fraction. An enzyme assay of the mt-nucleoid fraction showed that cytochrome c oxidase and fumarase activity were barely detected in the fraction, but the specific activity of KGDC in the mt-nucleoid fraction was relatively high and was approximately 60% of the specific activity in the mitochondrial fraction. Three components of KGDC were detected in the DNA-binding protein fractions after DNA-cellulose column chromatography of mt-nucleoid proteins. These results suggested that a part of KGDC in the mitochondrial matrix is associated with mt-nucleoids in vivo.

Acyltransferases↗

PubMed2002

Effects of the Min system on nucleoid segregation in Escherichia coli.

The Min system of Escherichia coli directs cell division to the mid-cell by a mechanism that involves the dynamic localization of all of its three constituent proteins, MinC, MinD and MinE. Both the Min system and the nucleoid regulate cell division negatively and strains of E. coli lacking a functional Min system can divide at nucleoid-free cell poles in addition to the nucleoid-free region between newly segregated nucleoids. Interestingly, E. coli strains with a defective Min system have disturbed nucleoid segregation and the cause for this disturbance is not known. It is reported here that growth conditions promoting a higher frequency of polar divisions also lead to a more pronounced disturbance in nucleoid segregation. In strains with an intact Min system, expression of MinE, but not of MinD, from an inducible promoter was followed by impaired nucleoid segregation. These results suggest that the disturbed nucleoid segregation in min mutants is not caused by polar divisions per se, nor by impaired resolution of chromosome dimers in min mutants, leaving open the possibility that the Min system has a direct effect on nucleoid segregation. It is also shown how the disturbed nucleoid segregation can explain in part the unexpected finding that the clear majority of cells in min mutant populations contain 2(n) (n=0, 1, 2.) origins of replication.

Adenosine Triphosphatases↗

PubMed1982

Structure of three-dimensionally rod-shaped mitochondrial nucleoids isolated from the slime mould Physarum polycephalum.

Mitochondrial nucleoids were isolated from microplasmodia of the true slime mould Physarum polycephalum using a discontinuous sucrose gradient following treatment of the mitochondria with Nonidet P-40. Studies of the isolated mitochondrial nucleoids by fluorescence and electron microscopy showed that the isolated structure was morphologically intact when compared with the structure in the mitochondria. Scanning and negative staining electron micrographs of the isolated mitochondrial nucleoids indicated the presence of 'elemental fibres', 10 nm in diameter, which were organized three-dimensionally into the rod-shaped structure of the nucleoid. Increases in ionic strength brought about loss of shape of the nucleoids and the elementary fibres became bare in places, from which thin filaments, believed to be DNA, protruded. After treatment of the isolated nucleoid with Pronase E, the three-dimensional shape was lost and a large number of DNA filaments appeared to radiate from the undigested region of the remaining nucleoid. Biochemical analyses of the isolated nucleoids revealed that the ratio of A235 to A260 was 0.7 while RNA:DNA and protein:DNA were 0.4 and 1.4, respectively. Sodium dodecyl sulphate/polyacrylamide gel electrophoresis of the isolated nucleoids indicated that polypeptides of molecular weight 20 K, 32 K, 34 K, 39 K, 41 K, 65 K, 66 K, 96 K and 125 K were associated specifically with the nucleoids.

DNA, Mitochondrial↗

PubMed2001

Behavior of plastid nucleoids during male gametogenesis in Plumbago auriculata.

We characterized the behavior of plastid (pt) and mitochondrial (mt) nucleoids during male gametogenesis in Plumbago auriculata in three dimensions. The behavior of pt-nucleoids and mt-nucleoids differed throughout male gametogenesis. Pt-nucleoids were distributed in a characteristic manner in three stages: in the early microspore, pt-nucleoids assemble around cell nucleus; in the mid-generative cell, pt-nucleoids gather at the internal side of the pollen; in the late-generative cell, pt-nucleoids aggregation turns its pole to the external side of the pollen. We also studied organelle nucleoids in the egg and the central cell by a method in which semi-thick sections of resin-embedded anthers and ovaries were observed by confocal laser scanning microscopy. The number of pt-nucleoids in the sperm cell did not differ significantly from that in the egg. These results suggest that the behavior of DNA-containing organelles is regulated strictly during male gametogenesis in P. auriculata, and that a biparental inheritance of plastids in the Plumbago embryo is more favored than was previously thought.

Cell Nucleus↗

PubMed2004

Studies on the compaction of isolated nucleoids from Escherichia coli.

The genomic DNA of Escherichia coli is contained in one or two compact bodies known as nucleoids. Isolation of typically shaped nucleoids requires control of DNA expansion, accomplished here by a modification of the polylysine-spermidine procedure. The ability to control expansion of in vitro nucleoids has application in nucleoid purification and in preparation of samples for high-resolution imaging, and may allow an increased resolution in gene localization studies. Polylysine of relatively low average molecular weight (approximately 3 kDa) is used to produce lysates containing nucleoids that are several-fold expanded relative to the sizes of in vivo nucleoids. These expanded forms can be converted to compact forms similar in dimensions to the cellular nucleoids by either a further addition of polylysine or by incubation of diluted lysates at 37 degrees C. The incubation at 37 degrees C is accompanied by autolytic degradation of most ribosomal RNA. Hyperchromism and circular dichroism spectra indicate that polylysine-DNA complexes are modified during the incubation. Compact forms of the nucleoid can be progressively reexpanded by exposure to salt solutions. Nucleoid compaction was similar in lysates made from rapidly or slowly growing cells or from cells that had been briefly treated with chloramphenicol to reduce linkages between DNA and cell envelope.

Chloramphenicol↗

PubMed1996

Isolation and characterization of mitochondrial nucleoids from the yeast Pichia jadinii.

Mitochondrial (mt) nucleoids were isolated with a high degree of purity from the yeast Pichia jadinii, in which the mitochondrial DNA (mtDNA) is linear. Field-inversion gel electrophoresis (FIGE) revealed that significant amounts of mtDNA could be isolated intact, as linear molecules of 41 kbp, from the isolated mt-nucleoids. Fifteen different proteins were detected in the mt-nucleoid fraction and, eight of these proteins bound to DNA. The patterns of mt-nucleoid proteins and of the DNA-binding proteins after gel electrophoresis in the presence of SDS were somewhat different from those of such proteins from Saccharomyces cerevisiae. The corresponding proteins isolated from the mt-nucleoids of four other species of yeast in the genera Pichia and Williopsis also differed from one another in terms of electrophoretic mobility in the presence of SDS. In immunoblotting experiments, antibodies that had been raised against the 67-kDa protein of mt-nucleoids from S.cerevisiae and the YMN-1 monoclonal antibody that is specific for a 48-kDa protein in the mt-nucleoids from S. cerevisiae did not recognize any proteins in the mt-nucleoids from Pichia jadinii and four other species of yeast. The results suggest the considerable diversity of the proteins in the mt-nucleoids of yeasts.

Animals↗

PubMed2005

Visualization of plastid nucleoids in situ using the PEND-GFP fusion protein.

Plastid DNA is a circular molecule of 120-150 kbp, which is organized into a protein-DNA complex called a nucleoid. Although various plastids other than chloroplasts exist, such as etioplasts, amyloplasts and chromoplasts, it is not easy to observe plastid nucleoids within the cells of many non-green tissues. The PEND (plastid envelope DNA-binding) protein is a DNA-binding protein in the inner envelope membrane of developing chloroplasts, and a DNA-binding domain called cbZIP is present at its N-terminus. We made various PEND-green fluorescent protein (GFP) fusion proteins using the cbZIP domains from various plants, and found that they were localized in the chloroplast nucleoids in transient expression in leaf protoplasts. In stable transformants of Arabidopsis thaliana, PEND-GFP fusion proteins were also localized in the nucleoids of various plastids. We have succeeded in visualizing plastid nucleoids in various intact tissues using this stable transformant. This technique is useful in root, flower and pollen, in which it had been difficult to observe plastid nucleoids. The relative arrangement of nucleoids within a chloroplast was kept unchanged when the chloroplast moved within a cell. During the division of plastid, nucleoids formed a network structure, which made possible equal partition of nucleoids.

Arabidopsis↗

PubMed2003

Compaction of the Escherichia coli nucleoid caused by Cyt1Aa.

Compaction of the Escherichia coli nucleoid in the cell's centre was associated with the loss of colony-forming ability; these effects were caused by induction of Cyt1Aa, the cytotoxic 27 kDa protein from Bacillus thuringiensis subsp. israelensis. Cyt1Aa-affected compaction of the nucleoids was delayed but eventually more intense than compaction caused by chloramphenicol. The possibility that small, compact nucleoids in Cyt1Aa-expressing cells resulted in DNA replication run-out and segregation following cell division was ruled out by measuring relative nucleoid length. Treatments with membrane-perforating substances other than Cyt1Aa did not cause such compaction of the nucleoids, but rather the nucleoids overexpanded to occupy nearly all of the cell volume. These findings support the suggestion that, in addition to its perforating ability, Cyt1Aa causes specific disruption of nucleoid associations with the cytoplasmic membrane. In situ immunofluorescence labelling with Alexa did not demonstrate a great amount of Cyt1Aa associated with the membrane. Clear separation between Alexa-labelled Cyt1Aa and 4',6-diamidino-2-phenylindole (DAPI)-stained DNA indicates that the nucleoid does not bind Cyt1Aa. Around 2 h after induction, nucleoids in Cyt1Aa-expressing cells started to decompact and expanded to fill the whole cell volume, most likely due to partial cell lysis without massive peptidoglycan destruction.

Bacillus thuringiensis↗

PubMed2006

Bacterial nucleoid dynamics: oxidative stress response in Staphylococcus aureus.

A single-molecule-imaging technique, atomic force microscopy (AFM) was applied to the analyses of the genome architecture of Staphylococcus aureus. The staphylococcal cells on a cover glass were subjected to a mild lysis procedure that had maintained the fundamental structural units in Escherichia coli. The nucleoids were found to consist of fibrous structures with diameters of 80 and 40 nm. This feature was shared with the E. coli nucleoid. However, whereas the E. coli nucleoid dynamically changed its structure to a highly compacted one towards the stationary phase, the S. aureus nucleoid never underwent such a tight compaction under a normal growth condition. Bioinformatic analysis suggested that this was attributable to the lack of IHF that regulate the expression of a nucleoid protein, Dps, required for nucleoid compaction in E. coli. On the other hand, under oxidative conditions, MrgA (a staphylococcal Dps homolog) was over-expressed and a drastic compaction of the nucleoid was detected. A knock-out mutant of the gene encoding the transcription factor (perR) constitutively expressed mrgA, and its nucleoid was compacted without the oxidative stresses. The regulatory mechanisms of Dps/MrgA expression and their biological significance were postulated in relation to the nucleoid compaction.

Bacterial Proteins↗

PubMed1999

Partitioning, movement, and positioning of nucleoids in Mycoplasma capricolum.

The nucleoids in Mycoplasma capricolum cells were visualized by phase-combined fluorescence microscopy of DAPI (4', 6-diamidino-2-phenylindole)-stained cells. Most growing cells in a rich medium had one or two nucleoids in a cell, and no anucleate cells were found. The nucleoids were positioned in the center in mononucleoid cells and at one-quarter and three-quarters of the cell length in binucleoid cells. These formations may have the purpose of ensuring delivery of replicated DNA to daughter cells. Internucleoid distances in binucleoid cells correlated with the cell lengths, and the relationship of DNA content to cell length showed that cell length depended on DNA content in binucleoid cells but not in mononucleoid cells. These observations suggest that cell elongation takes place in combination with nucleoid movement. Lipid synthesis was inhibited by transfer of cells to a medium lacking supplementation for lipid synthesis. The transferred cells immediately stopped dividing and elongated while regular spaces were maintained between the nucleoids for 1 h. After 1 h, the cells changed their shapes from rod-like to round, but the proportion of multinucleoid cells increased. Inhibition of protein synthesis by chloramphenicol induced nucleoid condensation and abnormal positioning, although partitioning was not inhibited. These results suggest that nucleoid partitioning does not require lipid or protein synthesis, while regular positioning requires both. When DNA replication was inhibited, the cells formed branches, and the nucleoids were positioned at the branching points. A model for the reproduction process of M. capricolum, including nucleoid migration and cell division, is discussed.

Bacterial Proteins↗

PubMed1976

Ultrastructural studies of the nucleoids of the pleomorphic forms of Chlamydia psittaci 6BC: a comparison with bacteria.

The nucleoids of the various pleomorphic forms of Chlamydia psittaci have been examined by direct observation of infected cells and by observations on isolated particles. The fixation and staining methods used were the same as those routinely used for the examination of bacteria to facilitate the comparison of chlamydial fine structure with that of bacteria. The nucleoids of reticulate bodies were composed of fine fibrils which extended throughout these particles. The nucleoids of intermediate bodies are characterized by an electron-dense mass with which the fibrous elements are associated in a structurally coherent manner. As condensation of the intermediate bodies proceeds, the electron-dense mass becomes eccentrically located and the fibers form a distinct radiating structure. Large elementary bodies have a few fibers associated with their condensed electron-dense nucleoids but the more condensed mature elementary bodies have a very discrete and homogeneous electron-dense nucleoid which is separated from the cytoplasmic elements of these particles by a very distinct electron-transparent space. These highly condensed elementary body nucleoids are usually ovoid, but may be elongated or irregular, and a small number of these structures react very strongly with ruthenium red. While the nucleoid structure of reticulate bodies resembles that of the bacterial cell, both the condensation process and the nucleoid morphologies which result from it in intermediate and elementary bodies have no parallels among the bacteria. Thus we conclude that major differences in nucleoid organization exist between the chlamydia and the bacteria.

Bacteria↗

PubMed1987

Isolation of morphologically intact mitochondrial nucleoids from the yeast, Saccharomyces cerevisiae.

Mitochondrial nucleoids (mt-nucleoids) of the yeast, Saccharomyces cerevisiae, were isolated from spheroplasts of stationary phase cells and their structure and organization were investigated by fluorescence microscopy, electron microscopy, and biochemical techniques. Isolated mt-nucleoids were spherical or ovoid and 0.3-0.6 micron in diameter, and were about the same size and shape as those observed in the cell by the DAPI staining technique. Measurement of DNA content of mt-nucleoids, using a video-intensified microscope system, after DAPI staining revealed that a mt-nucleoid in spheroplasts from stationary phase cells contains, on average, 3.9 mtDNA molecules and an isolated mt-nucleoid contains, on average, 3.1. Negatively stained electron micrographs showed that mt-nucleoids consist of particles 20-50 nm in diameter. SDS-polyacrylamide gel electrophoresis of mt-nucleoids detected 20 species of polypeptides in the molecular weight range from 10 X 10(3) to 70 X 10(3). Acid-urea/SDS two-dimensional electrophoresis of acid extract from mt-nucleoids indicated that a polypeptide of 20 X 10(3) is the only major polypeptide with basic property like histones.

DNA, Mitochondrial↗

PubMedDate not supplied

[Sedimentation of nucleoids from rat thymus and spleen cells following whole-body irradiation].

The sedimentation of nucleoids from thymic and splenic cells of rats was tested following total-body X-irradiation (TBI) with doses ranging from 24 to 1520 cGy. The principal results may be summarized as follows: 1) The nucleoid sedimentation of the cells was reduced immediately after TBI with doses of greater than or equal to 760 cGy. In the following postirradiation period, an enhancement of sedimentation rate has been observed which could be neutralized by addition of proteinase K to the nucleoid preparation. 2) When nucleoids were prepared 6 h after TBI with doses greater than or equal to 190 cGy, beside the main nucleoid band a smaller nucleoid fraction appeared in the ethidium bromide containing saccharose gradient. This fraction was of less sedimentability than the main nucleoid peak and could not be distinguished from pure, high molecular DNA. From the present results it is suggested that the reduction of the nucleoid sedimentation immediately following high doses of TBI is the result of primary (non-repaired) DNA lesions whereas the changes detectable some hours later are due to the secondary enzymatic changes connected with the interphase death of the cells. With respect to the detection of in vivo effects of X-irradiation, the nucleoid sedimentation has to be regarded much less sensitive than some biochemical and/or cytomorphological methods.

Animals↗

PubMed1995

Characterization of DNA-binding proteins involved in the assembly of mitochondrial nucleoids in the yeast Saccharomyces cerevisiae.

Mitochondrial nucleoids (mt-nucleoids) isolated from the yeast Saccharomyces cerevisiae were analyzed to identify the protein components that are involved in the compact packaging of mtDNA. The isolated mt-nucleoids were disassembled by the addition of 2 M NaCl and the disassembled mt-nucleoids were reassembled once again into compact structures by dialysis against a buffer that contained NaCl at concentrations below 0.1 M, as monitored by staining of the DNA with 4',6-diamidino-2-phenylindole. DNA-binding proteins with molecular masses of 67 kDa, 52 kDa, 50 kDa, 38 kDa, 30 kDa and 20 kDa were separated from isolated mt-nucleoids by column chromatography on DNA-cellulose after digestion of mt-nucleoids by DNase I in the presence or absence of 2 M NaCl. Purified mtDNA was compactly packaged into nucleoid-like structures upon the addition of fractions that contained DNA-binding proteins and subsequent dialysis to reduce the concentration of NaCl. Five proteins, with molecular masses of 67 kDa, 52 kDa, 50 kDa, 38 kDa and 30 kDa, respectively, had lower affinity for double-stranded DNA than that of the 20-kDa protein. The fraction that contained the five DNA-binding proteins other than the 20-kDa protein was also able to fold mtDNA compactly into nucleoid-like structures. By contrast, the combination of the 20-kDa protein and mtDNA resulted in formation of less tightly packed, string-of-bead structures. These results suggest that at least six different DNA-binding proteins are involved in the organization of the mt-nucleoids.

DNA, Fungal↗

PubMed1997

DNA gyrase involvement in chloroplast-nucleoid division in Cyanidioschyzon merolae.

Cyanidioschyzon merolae is a unicellular alga with one chloroplast and one mitochondrion per cell. Each of these organelles has a simple nucleoid located in the central area. Prior to mitosis and cytokinesis, both the division of organelle nucleoids and organellokinesis occur simultaneously. We investigated the effects of nalidixic acid, an inhibitor of DNA gyrase, on the replication and division of organelle nucleoids. Using microfluorometry, we monitored the synthesis of organelle DNA (organelle S phase) in synchronous cultures. In both the chloroplast and the mitochondrion, DNA synthesis occurred from the start of the light period and ceased within 3 h. The addition of nalidixic acid at the start of the light period inhibited DNA synthesis in both organelles. Next, we added nalidixic acid to the synchronous culture at the beginning (just before the organelle S phase) or at the end (organelle G2 phase) of the light period and monitored the division of organelle nucleoids in the dark period. Approximately 50 to 70% of chloroplast nucleoids divided unequally in both experiments. Despite the unequal division of the chloroplast nucleoids, electron microscopy revealed that the chloroplasts were divided into equal daughter chloroplasts by the chloroplast-divided ring. During the same treatments, all of the mitochondrial nucleoids underwent normal and equal division. Our results suggest the involvement of DNA gyrase in the replication of chloroplast and mitochondrial DNA and in the division of the chloroplast nucleoid, as well as a difference in mechanism between the division of chloroplast and mitochondrial nucleoids.

Anti-Infective Agents↗

PubMed1997

Isolation and characterization of spermidine nucleoids from Escherichia coli.

Nucleoids isolated from Escherichia coli at low salt concentrations in the presence of spermidine (Kornberg et al., Proc. Natl. Acad. Sci. USA, 71, 3189-3193 (1974)) retain large amounts of protein and RNA and are, thus, potentially useful in structural and other studies. However, these preparations have neither been visualized nor extensively characterized with regard to their protein and other components. We have investigated this type of nucleoid preparation and here supply both light and electron microscope appearances and a description of the DNA-associated proteins. Light microscopy is used to follow the stages of nucleoid release and to demonstrate characteristically rounded nucleoids after chloramphenicol treatment of the cells from which the nucleoids were isolated. The nucleoids are "envelope-associated" particles. Electron microscopy shows an irregular central core that is partially covered with small, membranous vesicles. A significant fraction of the nucleoids have a characteristic doublet/dumbbell-shaped appearance by light microscopy. The nucleoids contain large amounts of protein and RNA in addition to DNA. The DNA and RNA are rendered acid-soluble by very low levels of nucleases, indicating an open structure. A small group of proteins, including H-NS, FIS, HU, and RNA polymerase, is released from the particles upon enzymatic digestion of the DNA.

Bacterial Proteins↗

PubMed1982

Isolation and characterization of the nucleoid of non-complementing diploids from protoplast fusion in Bacillus subtilis.

Nucleoids of non-complementing diploids (Ncd) from protoplast fusion of B. subtilis were isolated. Their purified DNA banded in neutral CsCl gradient as a single unimodal peak of buoyant density 1.711 g/cm3, a value which is similar to that of the DNA purified from the original parental strains, suggesting that methylation of bases is not a significant factor in chromosome inactivation. Nucleoids released from a Ncd clone give two peaks in a sucrose gradient with a characteristic S value for each nucleoid. That is in contrast to nucleoids from the haploid parents whose sedimental patterns show only one peak. Both nucleoid preparations from Ncd strains assayed for transformation activity show the fast sedimenting nucleoid devoid of transformation activity while the slow nucleoid was active in transformation for the alleles carried by the genome which is expressed in vivo. Both nucleoids of the Ncd strains are transcribed in vivo. The RNA associated with the inactive chromosome is synthesized by the RNA polymerase of the active one. This study provides evidence that inactivation of one parental genome in the Ncd strain may be related with the tertiary organization of its DNA.

Bacillus subtilis↗