Organisation of genes for ribosomal RNA in Physarum polycephalum

Nucleotide sequence organisation and analysis of the nuclear ribosomal DNA circle of the protozoan parasite Entamoeba histolytica

We have sequenced the extrachromsomal ribosomal DNA (rDNA) circle of the human protozoan parasite Entamoeba histolytica HM-1:IMSS and present here the complete sequence organisation of the 24.5-kb molecule. Each circle contains two 5.9-kb rDNA transcription units organised as inverted repeats. The regions downstream (3543 bp) and upstream (9216 bp) of the rDNAs contain various families of short tandem repeats. Some of the upstream repeats share extensive sequence homology with the downstream repeats. In addition to the rDNAs themselves, the rDNA circle appears to code for only one other transcript which is 0.7 kb in size as seen in Northern blots. From DNA sequence analysis, no open reading frame could be assigned to the transcript. Extrachromosomal rDNA circles also exist in other E. histolytica strains. Restriction enzyme maps of rDNA circles were constructed from E. histolytica strains 200:NIH, HK-9 and Rahman; and Entamoeba moshkovskii strain Laredo. Striking differences were observed in the organisation of some of them, e.g. the HK-9, Rahman and Laredo circles contained only one rDNA unit and lacked the 0.7-kb transcript sequence. The short repeat sequences upstream and downstream of rDNAs were present in HK-9 and Rahman but absent in Laredo. Circles with one rDNA unit may be derived from those with two units by homologous recombination at direct repeat sequences located upstream and downstream of the two rDNAs.

Localization by high resolution in situ hybridization of the ribosomal minichromosomes during the nucleolar cycle of Physarum polycephalum

We have used biotinylated rDNA probes to localize by in situ hybridization the extrachromosomal genes for ribosomal RNA in the slime mold Physarum polycephalum. We established conditions that allow for highly specific hybridization at the ultrastructural level and determined that the 60-kb palindromic rDNA molecules are confined to the nucleolus in interphase. Our study definitively locates these extrachromosomal genes in mitosis in the form of thin DNA fibers contained within nucleolar remnants. We further show that these rDNA minichromosomes do not condense and that they segregate as entities independent of the condensed chromosomal DNA. In telophase, these minichromosomes migrate from the poles toward the equatorial region of the nucleus in a direction opposite that of the chromosomes. Our results illustrate the discontinuous nature of the nucleolar organizing region in Physarum.

Properties of isolated extrachromosomal nucleoli from Tetrahymena pyriformis

Extrachromosomal nucleoli were isolated from log phase cells of Tetrahymena pyriformis (amicronucleate strain) in a highly purified state. Nucleoli located at the periphery of the macronucleus were detached from the nucleoplasmic mass of isolated macronuclei with agitation and separated from macronuclei by filtration through a Nuclepore membrane filter (pore size 5 microm). The filtrate constitutes the crude nucleolar preparation, as judged by electron microscopy and DNA analysis. Further purification of the nucleoli was performed by isopycnic centrifugation of the filtrate in a Metrizamide density gradient. After this step, the purity of the nucleoli, as defined by rDNA content and measured by analytical CsCl centrifugation, was almost 100%. Electron microscopy of the purified nucleoli revealed structures that resemble those of an in situ nucleoli. Undegraded 35S pre-rRNA, together with 26S and 17S rRNA, could be isolated from purified nucleoli. In vitro RNA synthetic activity was associated with isolated nucleoli. This activity is insensitive to low and high concentrations of alpha-amanitin, indicating that the form I RNA polymerase is functioning.

Selective initiation of replication at origin sequences of the rDNA molecule of Physarum polycephalum using synchronous plasmodial extracts

A cell-free system using synchronous plasmodial extracts initiates replication selectively on the 60 kb rDNA palindrome of Physarum polycephalum. Preferential labeling of rDNA fragments by nuclear extracts, in which elongation is limited, indicates that initiation occurs at two positions corresponding to in vivo origins of replication estimated by electron microscopy. Both nuclear and whole plasmodial extracts initiate selectively within a plasmid, pPHR21, containing one of these origins. In this plasmid bubbles expand bidirectionally and generate DpnI-resistant DNA. Extracts made at prophase or early S phase, times when the nucleolus is disorganized, are most active in pPHR21 replication. Mapping positions of replication bubbles locates the initiation point in a 3.2 kb BstEII fragment at the upstream border of a series of 31 bp repeats 2.4 kb from the initiation point for ribosomal gene transcription.

rRNA genes of Naegleria gruberi are carried exclusively on a 14-kilobase-pair plasmid

An extrachromosomal DNA was discovered in Naegleria gruberi. The 3,000 to 5,000 copies per cell of this 14-kilobase-pair circular plasmid carry all the 18S, 28S, and 5.8S rRNA genes. The presence of the ribosomal DNA of an organism exclusively on a circular extrachromosomal element is without precedent, and Naegleria is only the third eucaryotic genus in which a nuclear plasmid DNA has been found.

Identification of the telomeric sequence of the acellular slime molds Didymium iridis and Physarum polycephalum

We have determined the telomeric DNA sequence of the acellular slime molds Didymium iridis and Physarum polycephalum. In both organisms the telomeres consist of tandem repeats of the hexamer 5'(TTAGGG)3'. This sequence was determined by cloning and sequencing the telomeric fragment of the linear extrachromosomal ribosomal DNA from Didymium, as well as direct end labeling and sequencing the rDNA from both organisms. Interestingly, this sequence is identical to the telomeric DNA sequence of the flagellated protozoan Trypanosoma brucei, and suggests that despite the diversity of telomeric sequences previously determined in lower eukaryotes, the necessity to create functional telomeres has led to constraints on these sequences.

rRNA genes of Naegleria gruberi are carried exclusively on a 14-kilobase-pair plasmid

An extrachromosomal DNA was discovered in Naegleria gruberi. The 3,000 to 5,000 copies per cell of this 14-kilobase-pair circular plasmid carry all the 18S, 28S, and 5.8S rRNA genes. The presence of the ribosomal DNA of an organism exclusively on a circular extrachromosomal element is without precedent, and Naegleria is only the third eucaryotic genus in which a nuclear plasmid DNA has been found.

Structure of the extrachromosomal ribosomal RNA chromatin of Physarum polycephalum

Isolated nucleoli from exponentially growing microplasmodia of Physarum polycephalum were digested with micrococcal nuclease or DNAase I, or were photoreacted with trimethyl psoralen. In the coding region for the precursor of the ribosomal RNA, micrococcal nuclease and DNAase I digestions show predominantly a smear, and treatment with psoralen leads to a fairly continuous crosslinking of the DNA. All three assays are compatible with the absence of a typical nucleosomal array in most of the gene copies. In contrast, in the central non-transcribed spacer, except in the immediate 5'-flanking region, micrococcal nuclease and DNAase I digestions yield fragments that are multiples of a basic repeat, compatible with a nucleosomal packing of this region. The crosslinking pattern with psoralen confirms this conclusion. In addition, there are three sites over 400 base-pairs long that are inaccessible for psoralen crosslinking. Two of these sites have been mapped to the putative origins of replication. In the terminal non-transcribed spacer, except in the immediate 3'-flanking region, digestions with micrococcal nuclease and DNAase I give a smeared repeat. The crosslinking pattern after treatment with psoralen suggests that this region is packed in nucleosomes, except for about 900 base-pairs constituting the telomere regions of the linear extrachromosomal palindromic rDNA. Micrococcal nuclease digestion of the immediate 5'-flanking region shows a complete absence of any nucleosomal repeat, but digestion with DNAase I leads to a faint ten base-pair repeat. In contrast, in the 3'-flanking regions both nuclease assays indicate a chromatin structure similar to the coding region. Both flanking regions are unusual with respect to psoralen crosslinking, in that crosslinking is reduced both in chromatin and deproteinized DNA. On the basis of the known sequence-dependent psoralen crosslinking and the established sequences in these regions, crosslinking should be expected to occur. However, it does not and we therefore propose the presence of an unusual DNA conformation in these regions.

Two-dimensional gel analysis of repetitive nuclear DNA sequences in the genome of Physarum polycephalum. Developmental regulation of the ribosomal gene number

The composition of repetitive sequences in restriction patterns of nuclear DNA of Physarum polycephalum was determined by high-resolution gel analysis. Three types of repeated DNA fragments in the size range of (0.2-2) X 10(3) base pairs could be identified as discrete spots on the gels and distinguished by their abundance and above-average base composition of either guanine and cytosine (G + C) or adenine and thymidine (A + T). On comparing the DNA composition from exponentially growing plasmodia with that of starved plasmodia, which have become competent to sporulate and have lost 80% of their nuclei, no change was detected among the (A + T)-rich repeat fractions, whereas several of the (G + C)-rich fractions revealed fewer copies in the DNA prepared from starved cells. As shown by hybridization under saturating conditions, the reduction of several (G + C)-rich repeated sequences in the restricted nuclear DNA in sporulation-competent cells can be explained by a 64% elimination of the extrachromosomal nucleolar ribosomal DNA sequences.

Processing in the external transcribed spacer of ribosomal RNA from Physarum polycephalum

The rDNA of the myxomycete Physarum polycephalum is transcribed to give a 13.3 kb precursor of ribosomal RNA. At 1.7 kb downstream of the primary initiation site there is a processing site or a second initiation site. This site was studied by S1-mapping, DNA sequencing and electron microscopy. None of these methods could conclusively distinguish between the two formal possibilities. However, capping experiments indicate that rapid processing is taking place at this site rather than reinitiation. In addition, primary transcripts and processed molecules were assayed throughout the synchronous mitotic cycle. During all interphase stages newly initiated transcripts of rDNA and products of the first processing step are present in similar amounts, indicating control of initiation and not of maturation as being the main regulatory step for the accumulation of mature rRNAs. During the brief period of mitosis the level of newly initiated rRNA precursors is lowered.

Faithful initiation of the in vitro transcription of a cloned rDNA from Tetrahymena pyriformis

A cloned rDNA fragment containing the transcriptional start point of Tetrahymena pyriformis was transcribed in vitro with a crude extract from homologous Tetrahymena cells. When a KpnI-HindIII fragment from the cloned rDNA plasmid was used as the template, the runoff transcription gave rise to two major RNA products about 490 and 460 nucleotides (nt) in length. An RNA of about 490 nt long was found to correspond to the expected transcript starting from the in vivo start point determined at our laboratory [Saiga et al., Nucl. Acids Res. 10 (1982) 4223-4235]. Precise size determination was performed using an RNA size marker prepared by hybridizing the template DNA with in vitro-capped 35S pre-rRNA followed by treatment with single-strand specific P1 nuclease. The size of the runoff transcript changed as predicted, according to downstream truncation points. The effects of alpha-amanitin and actinomycin D showed the transcription to be dependent on the added template DNA and to be catalyzed by form-I RNA polymerase. Possible reasons for the discrepancy between our determination of the size of the transcription product and that of Sutiphong et al. [Biochemistry 23 (1984) 6319-6326] are discussed.

Mapping of restriction enzyme cuts by a new two-dimensional procedure

A new procedure has been worked out to establish restriction maps. The method is fast, does not in general require labeled DNA and has been applied to map the linear palindromic rDNA of Physarum with the restriction enzyme Bst EII.

Direct repeats surrounding the ribosomal RNA genes of Physarum polycephalum

Sequence homology was found between the external transcribed spacer and the terminal non-transcribed spacer of Physarum polycephalum rDNA. The homologous sequences were located 2kb upstream from the 19s rRNA gene and 0.3kb downstream from 26S rRNA gene, respectively, and were arranged in a direct repeat manner. Sequence analyses showed that the direct repeats consisted of two parts: one was sequences of about 130bp which showed over 90% sequence homology with each other. The other consisted mainly of many tandem repeats of a 50 to 52bp unit. The direct repeat-rRNA genes-direct repeat unit was found to be flanked by short direct repetitious sequences. Based on these findings, the significance of the direct repeat is discussed in terms of evolution of rDNA.

Isolation and purification of transcriptionally active ribosomal chromatin from the slime mould, Physarum polycephalum

In the acellular slime mold Physarum polycephalum the ribosomal genes are all located on linear, extrachromosomal DNA molecules which are clustered in the nucleolus. This report describes the isolation and purification of these ribosomal genes as functionally active chromatin particles. Nucleolar lysates are fractionated by gel filtration to remove ribosomal precursors and other soluble material. The ribosomal chromatin is subsequently separated from contaminating nuclear chromatin by a sucrose gradient centrifugation step. This procedure allows the isolation of the ribosomal genes as intact nucleoprotein particles, which are now amenable to a biochemical analysis of their structural and functional properties.

5-Methyldeoxycytidine in the Physarum minichromosome containing the ribosomal RNA genes

5-Methyldeoxycytidine (5MC) was analyzed by high pressure liquid chromatography (HPLC) and by restriction enzyme digestion in rDNA isolated from Physarum polycephalum. rDNA from Physarum M3C strain microplasmodia has a significant 5MC content (about half that of the whole genomic DNA). This rDNA contains many C5MCGG sites because it is clearly digested further by Msp I than by Hpa II. However, most 5MC is in other sites. In particular, alternating CG sequences appear to be highly methylated. HPLC of deoxyribonucleosides shows tha most of the transcribed regions contain little or no 5MC. Restriction digestion indicates that there is little or no 5MC in any of the transcribed regions including the transcription origin and adjacent sequences. Over 90% of the total 5MC is in or near the central nontranscribed spacer and most methylated restriction sites are in inverted repeats of this spacer. rDNA is very heterogeneous with respect to 5MC. The 5MC pattern doesn't appear to change with inactivation of the rRNA genes during reversible differentiation from microplasmodia (growing) to microsclerotia (dormant), showing that inactivation is due to changes in other chromatin variables. The 5MC pattern is different between Physarum strains. The possible involvement of this 5MC in rDNA chromatin structure and in cruciform and Z-DNA formation is discussed.

Localization and DNA sequence around the initiation site of ribosomal RNA transcription in Physarum polycephalum

We have used S1 nuclease to map the initiation site of ribosomal RNA transcription in the acellular slime mold Physarum polycephalum, and we have determined the sequence of 1011 nucleotides surrounding the start site. Consistent with others' observations, there is little homology with the comparable region of other species. As predicted by previous restriction mapping, direct repeats roughly 30 base pairs in length are present upstream of the initiation site and a 148 base pair duplication occurs in the external transcribed spacer. The results also suggest the presence of a processing site within the external transcribed spacer of the ribosomal transcription unit.

Reversible changes in nucleosome structure and histone H3 accessibility in transcriptionally active and inactive states of rDNA chromatin

The sulfhydryl reagent iodoacetamidofluorescein (IAF) was used to probe the structure of chromatin subunits in transcribed and nontranscribed regions of Physarum rDNA. IAF labels histone H3 -SH groups in the elongated monomeric subunits (A particles) from the transcribed region, but it does not label H3 in the 11S monomers from the nontranscribed central spacer. All H3 reactivity is lost from rDNA chromatin in the inactive spherule stage of Physarum. Restriction cleavage of rDNA chromatin generates fragments from the transcription unit with reactive H3 -SH groups, whereas fragments containing nontranscribed spacer sequences are unreactive. The extended rDNA chromatin contains all four core histones and other prominent proteins. Electron microscopy shows that most of the extended subunits consist of two roughly spherical bodies connected by a 50 bp nucleoprotein bridge.

Structural homogeneity of mitochondrial DNA in the mitochondrial nucleoid of Physarum polycephalum

Mitochondrial DNA (mtDNA) of Physarum polycephalum was isolated gently by CsCl centrifugation. The mtDNA was linear with molecular weights ranging from 25 . 10(6) to 45 . 10(6) and heterogeneous in size. Nevertheless, thermal transition profiles of the mtDNA suggested that this DNA fraction was more homogeneous than nuclear DNA. Exhaustive digestions of this DNA with restriction endonucleases yielded unique fragments, and then the total of their molecular weights of each digest was around 45 . 10(6). This value is equivalent to the maximum molecular weight estimated using electron microscopy and electrophoresis. Moreover, EcoRI digests of the mtDNA fractionated by the sucrose gradient showed unequimolar quantities of large fragments and a high background between bands. These results suggest that the mtDNA of Physarum has a homogeneous base sequence, and that the size heterogeneity of the mtDNA is attributable to degradation of the DNA under isolation procedures. The mtDNA was cleaved by EcoRI and XhoI to yield 16 and 7 fragments, respectively. A physical map of these fragments was constructed using the routine mapping procedures. The physical map showed that the mitochondrial genome of Physarum was linear with molecular weight of 45 . 10(6). We concluded therefore that the mitochondrial nucleoid is a structure in which the homogeneous mtDNA is highly amplified.

Protein tightly bound near the termini of the Physarum extrachromosomal rDNA palindrome

The genes coding for ribosomal RNa in plasmodia of Physarum polycephalum are arranged palindromically on extrachromosomal rDNA molecules of 61 kb (kilobasepairs). Incubation of mildly extracted rDNA with the 125I Bolton-Hunter reagent results in incorporation of label not removed by SDS, CsCl, or various organic solvents. Labeled protein is preferentially associated with terminal rDNA restriction fragments, as detected after gel electrophoresis of the DNA. Antibody reaction with dinitrophenylated protein-rDNA complexes allows visualization of protein located from 1 to 2 kb from the termini, in a region containing multiple inverted repeat sequences and single-strand gaps. DNase I treatment of either rDNA or rDNA termini releases primarily two labeled protein bands of 5,000 and 13,000 daltons as well as less prominent bands of higher molecular weight. We discuss mechanisms for involvement of terminal protein in replication of 3' ends and chromosomal integration of the rDNA.

Different chromatin structures in Physarum polycephalum: a special form of transcriptionally active chromatin devoid of nucleosomal particles

Nonnucleolar chromatin from interphase nuclei of Physarum polycephalum plasmodia occurs in two different structural configurations as seen in electron microscopic spread preparations. While the majority of the chromatin is devoid of nascent ribonucleoprotein (RNP) fibrils and compacted into nucleosomal particles, a minor proportion (10-20%) is organized differently and reveals a smooth contour. It is this form of smooth chromatin which is rich in transcription units (mean length: 1.36 +/- 0.21 micrometer). Only occasionally are solitary nascent RNP fibrils observed which are associated with beaded strands of chromatin. In transcribed smooth chromatin nucleosomal particles are not only absent from the transcription units but also from their nontranscribed flanking regions, indicating that this special structural aspect is not merely a direct consequence of the transcriptional process. The existence of ca. 10-20% of Physarum chromatin in the smoothly contoured form is discussed in relation to reports of a preferential digestibility of a similar proportion of Physarum chromatin by DNAse I (Jalouzot et al., 1980) and to the altered configuration of "peak A" chromatin subunits after micrococcal nuclease digestion (Johnson et al., 1978 a, b).

Ribosomal ribonucleic acid repeat unit of Acanthamoeba castellanii: cloning and restriction endonuclease map

The repeat unit coding for the precursor to 18S, 5.8S, and 26S ribosomal ribonucleic acids (rRNAs) has been cloned from the free-living soil amoeba Acanthamoeba castellanii. The cloned deoxyribonucleic acid (DNA) was mapped with 11 restriction endonucleases and by R-loop mapping. The entire repeat unit is 12 kbp (kilobase pairs) in length and contains sites for EcoRI, SmaI, BglII, SstI, Bam-HI, PstI, KpnI, HindIII, and XbaI but not for XhoI or SalI. All of the repeat units in the nuclear DNA appear to be identical, and no introns were detected. However, the regions which code for the two RNAs which comprise the 26S RNA are separated by a gap of approximately 200 base pairs. Unlike some other lower eukaryotes, the 5S RNA gene is not linked to this repeat unit. A fragment of the repeat unit which contains the initiation sequence of the putative precursor has been subcloned into pBR322 for use in vitro transcription studies.

Sequence arrangement of the rRNA genes of the dipteran Sarcophaga bullata

Velocity sedimentation studies of RNA of Sarcophaga bullata show that the major rRNA species have sedimentation values of 26S and 18S. Analysis of the rRNA under denaturing conditions indicates that there is a hidden break centrally located in the 26S rRNA species. Saturation hybridization studies using total genomic DNA and rRNA show that 0.08% of the nuclear DNA is occupied by rRNA coding sequences and that the average repetition frequency of these coding sequences is approximately 144. The arrangement of the rRNA genes and their spacer sequences on long strands of purified rDNA was determined by the examination of the structure of rRNa:DNA hybrids in the electron microscope. Long DNA strands contain several gene sets (18S + 26S) with one repeat unit containing the following sequences in order given: (a) An 18S gene of length 2.12 kb, (b) an internal transcribed spacer of length 2.01 kb, which contains a short sequence that may code for a 5.8S rRNA, (c) A 26S gene of length 4.06 kb which, in 20% of the cases, contains an intron with an average length of 5.62 kb, and (d) an external spacer of average length of 9.23 kb.

A family of inverted repeat sequences and specific single-strand gaps at the termini of the Physarum rDNA palindrome

Ribosomal genes of Physarum polycephalum are located on multiple copies of an extrachromosomal, 61 kb rDNA palindrome. Each terminus of the palindrome consists of a nontranscribed spacer, averaging 5.4 kb in length, which includes a region of multiple inverted repeat sequences. Electron microscopy of denatured and reannealed termini reveals foldback segments that are multiples of a unit length of 50 bp, a length confirmed by sizing of restriction fragments from labeled termini. The total length of this inverted repeat region averages 600 bp per terminus, and the region is centered approximately 4 kb from the 3' end of the 26S gene. Restriction fragments containing the termini are heterogeneous, varying in length by +/- 400 bp. This heterogeneity is due to variability in both the number of 100 bp inverted repeats and the length of additional terminal spacer sequences. The inverted repeat region contains selectively located single-strand discontinuities as revealed by brief incubation with deoxynucleoside alpha-32P-triphosphates and E. coli DNA polymerase I (nick translation). Labelling at the discontinuities begins specifically with the sequence CCCTA. Discontinuities are nonligatable and are most likely gaps one nucleotide long. Each terminus contains 3 to 5 such gaps spaced approximately 200 bp apart. As measured by hybridization with selectively labeled foldback DNA, sequences homologous to the inverted repeats are widely distributed throughout chromosomal DNA.

Acetylation of histone H4 and its role in chromatin structure and function

Histone h4 is a highly conserved structural component of the nucleosome subunit of chromatin. The activation of chromatin is accompanied by changes in structure which may be caused by histone modification or by interactions of specific non-histone proteins, or both. Histone H4 can be modified by acetylation and this modification has been correlated with chromosome assembly and with transcription. We have now tested these correlations by studying H4 acetate content as a function of the cell cycle using the naturally synchronous cell cycle in Physarum polycephalum. The results show two clear correlations: (1) tetra-acetylated H4 correlates with transcription; (2) highly acetylated H4 (2 to 4 acetates per molecule) is inversely correlated with H1 phosphorylation and initiation of chromosome condensation in prophase. The results are consistent with turnover of di-acetylated H4 during chromosome assembly in S phase.

Processing of ribosomal precursor RNAs in Physarum polycephalum

The processing of intermediates of Physarum rRNA has been investigated using two cloned rDNA restriction fragments as sequence specific probes. The size of the largest stable pre-rRNA detected is 11.8 Kb, as determined by denaturing gel electrophoresis. R-loop analysis revealed that this pre-rRNA fraction mainly consists of transcripts which do not contain the two insertion sequences present in the 26 S gene. However, a small number of molecules are found which still contain one or the other, or both, of these introns. These observations suggest that the two introns are transcribed but spliced out in a random order before RNA synthesis has reached the 3-end of the primary transcript. Transcription starts at about 17.7 Kb and stops at 4.4 Kb as measured from the ends of the linear palindromic rDNA molecule. Besides the 11.8 Kb transcript several further ribosomal RNA precursors have been identified, ranging in size from 2.5 to 8.8 Kb. In addition, the genes for 5.8 S RNA have been located by R-loop mapping.

Organization of ribosomal genes in Paramecium tetraurelia

The macronuclear ribosomal DNA (rDNA) of the ciliated protozoan Paramecium tetraurelia (stock 51) was analyzed by digestion with restriction endonucleases. The fragments which contained ribosomal RNA (rRNA) coding sequences and spacer sequences were identified. The spacer sequences exhibited some heterogeneity in size. The genes coding for 5.8S RNA, but not for 5S RNA, are linked to the 17S and 25S rRNA genes. Complementary RNA, synthesized from rDNA of stock 51, was hybridized with restriction digests of whole cell DNA from six other allopatric stocks of this species. The restriction patterns of the rDNA from these seven stocks were, in general, very similar, and the sizes of the coding sequences were identical in all seven stocks. Only the restriction pattern of rDNA from stock 127 differed significantly from that of stock 51. The rDNA from stock 127 was isolated and characterized, and with the exception of the restriction pattern of its spacer, it resembled the rDNA from stock 51. It is concluded that the rDNA repeat in Paramecium, including the spacer, has, in general, been conserved during the course of evolution. It is suggested that in some species, even in the absence of genetic exchange among geographically separated populations, selection pressure may act to conserve spacers of tandemly repeated rDNA. The conservation may be related to the number of rDNA copies in the germinal nucleus.

Different nucleosome structures on transcribing and nontranscribing ribosomal gene sequences

Monomeric DNA lengths from Physarum nuclear chromatin occur in two subunit forms which differ from each other and from higher oligomers of nucleosomes in content of transcribed ribosomal DNA sequences. Labeled DNA restriction fragments from ribosomal RNA coding regions reanneal most rapidly with DNA from a monomeric subunit fraction. A particles, isolated from growing plasmodia and containing 144 base pairs of DNA in an extended conformation. Higher oligomers of nucleosomes are depleted in sequences from transcribing gene regions but are enriched in sequences from the nontranscribed central spacer of the ribosomal DNA palindrome. Nucleosome configuration on two 26S gene intervening sequences resembles that on adjacent coding regions.

A study of the organisation of the ribosomal ribonucleic acid gene cluster of Neurospora crassa by means of restriction endonuclease analysis and cloning in bacteriophage lambda

1. Total Neurospora crassa DNA was restricted with endonucleases and fragments carrying rRNA coding sequences were identified by hybridization with Xenopus laevis ribosomal DNA probes. 2. The repeating unit of the rRNA gene cluster was found to be 8.6 kbp, arranged in a head-to-tail fashion. 3. Digestion with Hind III yielded fragments of 3.4 kbp and 5.2 kbp and both were cloned. 4. Digestion with Eco RI yielded fragments of 2.2 kbp, 3.0 kbp and 3.4 kbp; the 3.0 kbp fragment was cloned. 5. Sequences coding for RNA (S-rRNA)1 of the smaller subribosomal particle were found (at least 90%) in the 2.2 kbp EcoRI subfragment of the 5.2 kbp Hind III fragment. 6. The coding sequences for the major RNA species (L-rRNA) of the larger subribosomal particle were located mainly (at least 95%) in the 3.4 kbp Hind III fragment. 7. For comparison, a Hind III digest of total yeast DNA was cloned and recombinants containing a 6.4 kbp rDNA fragment were isolated.

Characterisation of ribosomal satellite in total nuclear DNA from Physarum polycephalum

The distinctive properties of satellite DNA molecules containing the genes for ribosomal RNA in Physarum polycephalum permits their identification in total, unfractionated nuclear DNA in the foldback form, after denaturation and fast annealing. Using the electron microscope the location and properties of three characteristic regions containing tandemly-repeated, inverted sequences have been investigated. At least two additional regions, also containing tandem repeats, are shown to be present and located towards each end of the rDNA molecule, at a site adjacent to the segment coding for the 26 S rRNA. All the regions which contain tandem repeats are composed of sequences which, within experimental error, appear to share a common unit repeat length of about 90 nucleotides.

Arrangement of the genes coding for ribosomal ribonucleic acids in Neurospora crassa

We have cloned and characterized Neurospora crassa ribosomal deoxyribonucleic acid (rDNA). The rDNA is found as a tandemly repeated 6.0-megadalton sequence. We have mapped a portion of the rDNA repeat unit with respect to its sites for 13 restriction endonucleases and defined those regions coding for the 5. 8S, 17S, and 26S ribosomal ribonucleic acids (rRNA's). We have also isolated several clones containing 5S rRNA sequences. The 5S rRNA coding sequences are not found within the rDNA repeat unit. We found that the sequences surrounding the 5S rRNA coding regions are highly heterogeneous.

Accessibility of the ribosomal genes to micrococcal nuclease in Physarum polycephalum

In Physarum polycephalum most genes coding for ribosomal RNA are not integrated in chromosomes, but are located in many copies in the nucleolus as plasmid-like palindromic DNA molecules. To find out whether coding sequences of rDNA are organized in a chromatin-like structure similar to that of bulk chromatin, nuclei were treated with micrococcal nuclease and DNA fragments were isolated. From bulk chromatin multimers of a basic unit of 170-180 base pairs were obtained. Nuclease fragmented DNA hybridized with labelled 19-S + 26-S rRNA was found to give the same saturation value as did unfragmented control DNA. No preferential degradation of ribosomal genes to acid soluble products was observed. A more detailed analysis of the nuclease degradation products was carried out with fragments separated by preparative gel electrophoresis. DNA eluted from the gels was hybridized in solution with labelled 19-S + 26-S rRNA. The coding sequences of rRNA were found to be degraded to approximately nucleosome size slightly more quickly than was the DNA of bulk chromatin. However, the distribution of the rDNA fragments on the gels did not coincide with the distribution of the fragments derived from bulk chromatin nucleosomes and their oligomers. The amount of rDNA in the interband regions was about intermediate between that found in the two adjacent bands. These results lead to the conclusion that the ribosomal genes, most of which are presumably active during rapid growth, are protected by proteins, probably histones. However, the ribosomal genes are present in a structure differing in some way from that of bulk chromatin.

Size distribution and maturation of newly replicated DNA through the S and G2 phases of Physarum polycephalum

The size distribution of newly made DNA and the dynamics of size maturation of progeny DNA molecules were studied in the synchronous S and G2 phases of Physarum polycephalum. Pulse labeling of DNA and analysis of the products on alkaline sucrose gradients showed that synthesis of primary replication units (which will also be referred to as "Okazaki" fragments) occurred throughout the S period. Pulse and pulse-chase experiments revealed a distinct pattern of size maturation. An apparently linear increase in molecular weight of progeny DNA molecules during the first hour of the S phase occurred at a rate of approximately 4-5 X 10(5) daltons per min at 26 degrees C, corresponding to the joining of 6-8 Okazaki fragments. The resulting 35-45S (1.1-2.2 X 10(7) daltons) DNA molecules may correspond to the Physarum "replicon." The further size increases of the newly made DNA appear to occur in steps, possibly reflecting a clustering of isochronous replicons along the chromatide. These observations are discussed with regard to mechanisms of DNA replication and size maturation.

Ribosomal genes in Physarum polycephalum: transcribed and non-transcribed sequences have similar base compositions

The transcribed and non-transcribed sequences in Physarum polycephalum ribosomal DNA (rDNA) were separated by restriction nuclease digestion of pure rDNA and the products fractionated by zone sedimentation in sucrose gradients. The base compositions of the fragments were determined by analytical centrifugation in CsCl or in CsCl with netropsin. All the fragments had dA + dT contents in the range 44-48%. From the known sequence arrangement and transcription pattern of Physarum rDNA it was concluded that coding sequences, transcribed but non-coding sequences, and non-transcribed sequences all possess similar base compositions, contrary to the situation in many other systems. The thermal denaturation profile of Physarum rDNA is reported. It suggests the rDNA sequence is complex and supports the above conclusion of limited heterogeneity of base composition.

Ribosomal DNA in spores of Physarum polycephalum

DNA was isolated from plasmodia, spores and newly hatched amoebae of the slime mould Physarum polycephalum. The DNA preparations were fractionated in CsCl gradients and each fraction hybridised to combined 19 S + 26 S rRNA. In all three DNA preparations hybridisation was found to be limited to satellite DNA (rho = 1.714 g/cm3) and at saturation was found to reach a level of 0.16--0.18 % of total DNA. The main band of nuclear DNA (rho = 1.702 g/cm3) did not hybridise appreciably. Further experiments using analytical CsCl gradients revealed that the ratio of satellite to main band DNA was similar in all three preparations. It is concluded that the genes for ribosomal RNA are equally reiterated in spores, hatching amoebae and in plasmodia. They appear to be similarly organised in all stages of the life cycle examined so far.

Metabolic stability of the extrachromosomal ribosomal RNA genes in the slime mould Physarum polycephalum

The rRNA genes of the slime mould Physarum polycephalum are located on free, linear DNA molecules of a discrete size, Mr=38X10(6). Using an isotope dilution technique we have examined the metabolic stability of these extrachromosomal genes during active, balanced growth. Microplasmodia, prelabelled with [3H]thymidine, were used to prepare synchronous surface plasmodial cultures which were subsequently grown on unlabelled medium. The gross synthesis of ribosomal DNA was then determined over three consecutive mitotic divisions from the ratio of 3H to 14C in a hybrid formed between the extracted ribosomal [3H]DNA and a [14C]rRNA probe. It was found that ribosomal DNA, like chromosomal DNA, is completely stable during active growth.