PCR amplification of the 3'' external transcribed and intergenic spacers of the ribosomal DNA repeat unit in three species of Saccharomyces

Abstract Desulfotomaculum thermobenzoicum TSB converted 4 mol pyruvate to 5 mol acetate in the absence of sulfate. The cells grown on pyruvate without sulfate showed both carbon monoxide dehydrogenase (CODH) and methylmalonyl-CoA: pyruvate transcarboxylase activities. However, considering the fermentation products, the acetogenesis from pyruvate might be conducted by CODH pathway rather than methylmalonyl-CoA pathway. Contrary to this finding, Desulfobulbus propionicus MUD fermented 3 mol pyruvate to 2 mol acetate and 1 mol propionate stoichiometrically via methylmalonyl-CoA pathway. Desulfovibrio vulgaris Marburg, which has neither the CODH pathway nor the methylmalonyl-CoA pathway, converted pyruvate to acetate, H₂ and CO₂ as the main products. These results indicate that the fermentation pattern of pyruvate depends on the metabolic characteristics of each sulfate-reducing bacterium.     

Polymorphisms in the intergenic region of the sea urchin Paracentrotus lividus ribosomal DNA

Blot-hybridizations of the sea urchin Paracentrotus lividus genomic DNA with ribosomal DNA (rDNA) probes revealed individual variations in the length and in the sequence of the non-transcribed spacer (NTS) region. The number of rDNA repeat subclasses distinguishable within any individual sea urchin is usually limited (1 to 3) with respect to the widest polymorphism of the population as a whole. The heterogeneity in sequence is revealed by the presence or the absence of specific restriction sites in the spacer region. The data obtained by the intensity of the polymorphic bands indicate that different mechanisms bring about these two types of polymorphism. Preliminary data also indicate different methylation patterns in single individuals.     

High-frequency intragenomic heterogeneity of the ribosomal DNA intergenic spacer region in Trichophyton violaceum

The intergenic spacer (IGS) of the rRNA genes was analyzed from the dermatophyte Trichophyton violaceum isolated from cases of tinea capitis in Taiwan and Iran. T. violaceum strains were cultured from different colonies, from single conidial colonies derived by dilution plating, and from micromanipulation of single conidia from clinical samples. A ribosomal DNA probe hybridizing to multiple EcoRI fragments was used to compare restriction fragment length polymorphisms in different T. violaceum isolates. The arthroconidia of T. violaceum that form in vivo during infection were shown to contain a single nucleus by 4',6'-diamidino-2-phenylindole staining. IGS regions from an isolate cultured from a single conidium were amplified, cloned, and sequenced. The results identified that heterogeneity exists between IGS regions within a single T. violaceum genome due to different copy numbers of a 171-bp tandem repeat. This suggests that the IGS of T. violaceum is partially excluded from the concerted evolution of the rRNA gene locus. The heterogeneous character of the IGS regions in T. violaceum contrasts with the closely related dermatophyte Trichophyton rubrum, posing further questions on the phylogeny and the evolution of dermatophyte fungi.     

Structure and evolution of the 4.5-5S ribosomal RNA intergenic region from Glycine max (soya bean).

The nucleotide sequence for the 4.5-5S ribosomal DNA region from the chloroplastids of soya beans was determined as the basis of further comparative studies on the structure and evolution of this intergenic region. Comparisons with other plant sequences as well as equivalent sequences in eubacteria suggest that the longer internal transcribed spacer regions of plants have evolved, at least in part, by DNA sequence duplications and that the presence of the 4.5S rRNA in chloroplast may result from the accidental acquisition of a RNA maturation site during the evolution of longer internal transcribed spacer regions. Estimates of the secondary structures also indicate only a very limited retention of structural features and suggest that the primary role of the intergenic sequences may be to bring processed sites into close proximity.     

PCR amplification and characterization of the intergenic spacer region of the ribosomal DNA in Pyrenophora graminea

Successful amplification of the whole intergenic spacer region of the nuclear ribosomal repeat (IGS) in Pyrenophora graminea was obtained with a PCR-based assay. Single amplification products showed length differences. Depending on the length of the IGS-PCR product, ca. 3.8 or 4.4 kb, two groups of isolates could be identified. The RFLP patterns of isolates obtained with the 6-base cutting enzymes ApaI, BglII, DraI, EcoRV, HindIII and SacI were similar within each group and different between the two groups. Restriction patterns of IGS-PCR products digested with the 4-base cutting enzyme AluI were polymorphic among isolates in spite of their IGS-PCR product length. In order to characterize the long and short IGS-PCR products the restriction map is shown. The long product shows an additional HindIII site and a BglII site that is lacking in the short product. However, the latter shows a SacI site that is not present in the long IGS-PCR product. Therefore, the described PCR-RFLP analysis of the IGS appears to be a useful tool to resolve genetic variation between P. graminea isolates.     

A physical map of the ribosomal DNA repeat unit of Aspergillus nidulans

The ribosomal DNA repeat unit of Aspergillus nidulans has been cloned in pBR322 and a restriction map constructed. The genes coding for the 17S, 5.8S and 25S rRNAs are found in blocks separated by a 1.7 kb spacer region, with the 5.8S RNA gene lying between the genes for the two larger RNAs. The total length of the repeat unit is 7.7 kb. The 5S rRNA is not present in the repeat unit.     

Antigen expression from the ribosomal DNA repeat unit of Giardia intestinalis.

The amitochondrial human intestinal parasite Giardia intestinalis is regarded to be the most ancient living example of single-celled eukaryotes and should display primitive features of pre-metazoan gene regulation. Characterization of E. coli clones which express Giardia antigens from plasmid vectors has revealed that an antigen is encoded by the rDNA repeat unit from the strand complementary to that encoding the rRNAs. The open reading frame (ORF) originates in the spacer region between the small (SS) and large (LS) subunit rRNA genes and terminates within the LS rRNA gene. The promoter region of this ORF has characteristics of both RNA polymerase (pol) II and pol III regulatory sequences, suggestive of gene regulation before these different promoter types evolved. The rDNA repeat unit is located on multiple chromosomal sites which are different in each isolate, although the electrophoretic karyotypes appear very stable in Giardia from both human and animal sources.     

PCR amplification and polymorphism analysis of the intergenic spacer region of ribosomal DNA in Tuber borchii

PCR amplification of the complete intergenic spacer region (IGS) of the Tuber borchii nuclear ribosomal repeat was obtained using universal primers CNL 12 and NS1rev. In order to improve amplification yield a specific primer, T1, was selected from a partial sequence of the IGS product. IGS diversity was characterized both at the intraindividual and intraspecific level. The results obtained at the intraindividual level showed 10% varying repeats on ten screened colonies, while at the intraspecific level the IGS polymorphism was evident as difference in length amplification between mycelial strains and fruit bodies: 3.5 kb and 2 kb respectively.     

Zea ribosomal repeat evolution and substitution patterns

Zea and Tripsacum nuclear ribosomal internal transcribed spacer (ITS) sequences were used to evaluate patterns of concerted evolution, rates of substitutions, patterns of methylation-induced deamination, and structural constraints of the ITS. ITS pseudogenes were identified by their phylogenetic position, differences in nucleotide composition, extensive deamination at ancestral methylation sites, and substitutions resulting in low-stability secondary RNA structures. Selection was important in shaping the kinds of polymorphisms and substitutions observed in the ITS. ITS substitution rates were significantly different among the Zea taxa. Deamination of cytosines at methylation sites was a potent mutation source, but selection appeared to maintain high methylation site density throughout the ribosomal repeat except for the gene promoter. Nucleotide divergence statistics identified selectively constrained regions at the 5' ends of the ITS1 and ITS2.      

Evolution and phylogenetic information content of the ribosomal DNA repeat unit in the Blattodea (Insecta)

The organization, structure, and nucleotide variability of the ribosomal repeat unit was compared among families, genera, and species of cockroaches (Insecta:Blattodea). Sequence comparisons and molecular phylogenetic analyses were used to describe rDNA repeat unit variation at differing taxonomic levels. A reverse similar 1200 bp fragment of the 28S rDNA sequence was assessed for its potential utility in reconstructing higher-level phylogenetic relationships in cockroaches. Parsimony and maximum likelihood analyses of these data strongly support the expected pattern of relationships among cockroach groups. The examined 5' end of the 28S rDNA is shown to be an informative marker for larger studies of cockroach phylogeny. Comparative analysis of the nucleotide sequences of the rDNA internal transcribed spacers (ITS1 and ITS2) among closely related species of Blattella and Periplaneta reveals that ITS sequences can vary widely in primary sequence, length, and folding pattern. Secondary structure estimates for the ITS region of Blattella species indicate that variation in this spacer region can also influence the folding pattern of the 5.8S subunit. These results support the idea that ITS sequences play an important role in the stability and function of the rRNA cluster.     

Aspects of nonrandom turnover involved in the concerted evolution of intergenic spacers within the ribosomal DNA of Drosophila melanogaster

Polymerase chain reaction (PCR)-amplified, sequenced, and digitally typed intergenic spacers (IGSs) of the ribosomal (r)DNA in D. melanogaster reveal unexpected features of the mechanisms of turnover involved with the concerted evolution of the gene family. Characterization of the structure of three isolated IGS length variants reveals breakage hot spots within the 330-base-pair (bp) subrepeat array found in the spacers. Internal mapping of variant repeats within the 240-bp subrepeat array using a novel digital DNA typing procedure (minisatellite variant repeat [MVR]-PCR) shows an unexpected pattern of clustering of variant repeats. Each 240-bp subrepeat array consists of essentially two halves with the repeats in each half identified by specific mutations. This bipartite structure, observed in a cloned IGS unit, in the majority of genomic DNA of laboratory and wild flies and in PCR-amplified products, has been widely homogenized yet is not predicted by a model of unequal crossing over with randomly placed recombination breakpoints. Furthermore, wild populations contain large numbers of length variants in contrast to uniformly shared length variants in laboratory stocks. High numbers of length variants coupled to the observation of a homogenized bipartite structure of the 240-bp subrepeat array suggest that the unit of turnover and homogenization is smaller than the IGS and might involve gene conversion. The use of PCR for the structural analysis of members of the rDNA gene family coupled to digital DNA typing provides powerful new inroads into the mechanisms of DNA turnover affecting the course of molecular evolution in this family. Correspondence to: G. A. Dover     

The intergenic spacer region of the ribosomal RNA gene of Penicillium marneffei shows almost no DNA sequence diversity

The fungus Penicillium marneffei causes fatal systemic infections and is endemic in many parts of South-East Asia, especially Thailand. The intergenic spacer (IGS) region, the most variable region of rRNA genes, was found to be highly conserved among 58 P. marneffei strains. IGS analysis might not be suitable for molecular epidemiological analysis of P. marneffei infections.     

Structure of the central spacer region of extrachromosomal ribosomal DNA in Physarum polycephalum

We have analyzed the sequence organization of the central spacer region of the extrachromosomal ribosomal DNA from two strains of the acellular slime mold Physarum polycephalum. It had been inferred previously from electron microscopy that this region, which comprises about one third of the 60 kb³ palindromic rDNA, contains a complex series of inverted repetitious sequences. By partial digestion of end-labeled fragments isolated from purified rDNA and from rDNA fragments cloned in Escherichia coli, we have constructed a detailed restriction map of this region. The 11 kb of spacer DNA of each half molecule of rDNA contains the following elements: (a) two separate regions, one of 1.1 kb and one of 2.1 kb, composed of many direct repeats of the same 30 base-pair unit; (b) a region of 4.4 kb composed of a complex series of inverted repeats of a 310 base-pair unit; (c) another region of 1.6 kb composed of inverted repeats of the same 310 base-pair unit located directly adjacent to the center of the rDNA; (d) two copies of a unique sequence of 0.85 kb, which probably contains a replication origin. Some of the CpG sequences in the spacer resist cleavage by certain restriction endonucleases and thus appear to be methylated. The lack of perfect symmetry about the central axis and the arrangement of inverted repeated sequences explain the complex pattern of branches and forks of the fold-back molecules previously observed by electron microscopy. Comparison of the rDNA restriction maps from the two strains of Physarum suggests that the repeat units in the spacer are undergoing concerted evolution. We propose a model to explain the evolutionary origin of the several palindromic axes in the Physarum rDNA spacer.     

Structure of the intergenic spacer region from the ribosomal RNA gene family of white spruce (Picea glauca)

Five genomic clones containing ribosomal DNA repeats from the gymnosperm white spruce (Picea glauca) have been isolated and characterized by restriction enzyme analysis. No nucleotide variation or length variation was detected within the region encoding the ribosomal RNAs. Four clones which contained the intergenic spacer (IGS) region from different rDNA repeats were further characterized to reveal the sub-repeat structure within the IGS. The sub-repeats were unusually long, ranging from 540 to 990 bp but in all other respects the structure of the IGS was very similar to the organization of the IGS from wheat, Drosophila and Xenopus.