Polymorphism for ribosomal RNA gene arrangement in the mitochondrial genome of fall rye (Secale cereale L.)

A restriction-fragment-length polymorphism (RFLP) in mitochondrial DNA (mtDNA) was detected between varieties of fall rye (Secale cereale L.) by Southern hybridization with rrn18, the gene encoding the mitochondrial 18S ribosomal RNA. Restriction mapping showed that the RFLP is based on differing numbers of genomic contexts (one vs three) for a recombining-repeat element (the 18S/5S repeat). From examination of other Secale species, we conclude that the one-context state arose relatively recently, putatively by deletion of two of an ancestral set of three distinct genomic loci containing the mitochondrial 18S/5S repeat. This is consistent with our earlier conclusion that the 18S/5S repeat has probably existed in at least two genomic copies throughout much of the history of the grass family (at least 40 million years). Interestingly, the intervarietal difference in the number of distinct rrn18 loci is not accompanied by a major difference in the number of rrn18 copies per unit mass of mtDNA. This suggests the existence of a mechanism that can compensate rather precisely for differences in mitochondrial gene dosage, perhaps by over-replication or stabilization of specific subgenomic molecules.     

Nucleotide sequence and determination of the extremities of the 26S ribosomal RNA gene in wheat mitochondria: evidence for sequence rearrangements in the ribosomal genes of higher plants

Summary The nucleotide sequence of the wheat mitochondrial 26S ribosomal RNA gene and flanking regions was determined and compared with mitochondrial 26S rRNA genes from maize and Oenothera. All three genes exhibit a high degree of homology except within two variable regions. When the plant mitochondrial 26S rRNA genes are compared with Escherichia coli 23S rRNA and chloroplast 23S and 4.5S rRNA genes, a third variable region is apparent close to the 3 end of the gene. The 5 and 3 ends of the wheat mitochondrial gene were determined by S1 nuclease mapping. Computer analysis of the wheat mitochondrial gene revealed several small sequences present either in the 5 region of the 26S rRNA gene or in the 18S rRNA gene.     

Organization of the 5.8S, 16–18S,and 23–28S ribosomal RNA genes of Cephalosporium acremonium

Summary A 9.2 kb Pst1 restriction fragment, repeated tandemly head-to-tail in the genome, contains the 5.8S, 16–18S, and 23–28S ribosomal RNA (rRNA) genes of Cephalosporium acremonium, a filamentous fungus used at the industrial scale for production of cephalosporin antibiotics. These rRNA genes were located in Pst1 digests of C. acremonium genomic DNA using a hybridization probe that contained the 5.8S, 18S, and 25S rRNA genes from the yeast Saccharomyces cerevisiae. This probe was also used in screening a recombinant lambda library to identify phage carrying rRNA genes of C. acremonium. Yeast rRNA genes contained separately on individual ³²P-labeled plasmids were used to demonstrate that a cloned 7.2 kb C. acremonium sequence, represented in the repeated 9.2 kb Pst1 fragment, contained DNA from the C. acremonium 5.8S, 16–18S, and 23–28S rRNA genes. These genes were ordered with the 5.8S gene located between the 16–18S and 23–28S rRNA genes. The order of the 16–18S, 5.8S, and 23–28S rRNA genes observed in C. acremonium is the same as that observed in rRNA repeats of many other lower eucaryotes, e.g. S. cerevisiae, Aspergillus nidulans, and Neurospora crassa.     

Unusual organization and lack of recombination in the ribosomal RNA genes of Coprinus cinereus

Summary We find three interesting characteristics of the genes encoding the ribosomal RNA (rRNA) in the basidiomycete Coprinus cinereus. First, there are only 60 to 90 copies of the genes, fewer than in other fungi. Second, the genes are organized in an unusual arrangement. The 5S rRNA genes are located in the repeat unit which encodes the other rRNAs and all four rRNAs are transcribed in the same direction. Third, meiotic recombination is inhibited within the ribosomal DNA.     

The organization of the genes for ribosomal RNA on mitochondrial DNA of Kluyveromyces lactis

Summary We have constructed a physical map of Kluyveromyces lactis mtDNA using the restriction enzymes HindII and HindIII. In contrast to Saccharomyces, the genes for the large and small ribosomal RNAs are much closer to each other, being separated by a maximal distance of 2,250 base pairs.Abbreviations bp base pair(s) - rRNA ribosomal RNA - SSC 0.15 M NaCl, 0.015 M sodium citrate (pH 7.0)     

Nuclear genes control changes in the organization of the mitochondrial genome in tissue cultures derived from immature embryos of wheat

Summary Although the mitochondrial genomes of the Chinese Spring and Aquila varieties of wheat are normaly similar in organization, this is not so in tissue cultures initiated from their immature embryos where the mitochondrial genomes of both are rearranged and in different, characteristic, ways. However, the mitochondrial genomes of tissue cultures of reciprocal F₁ crosses between these varieties were almost identical to one another, showing that nuclear genes control the rearrangement processes. These rearrangements are either due to the appearance of new structures or else result from changes in the relative amounts of subgenomic components. The severe reduction in the amount of certain molecular configurations in tissue cultures from reciprocal crosses is probably due to the presence of dominant information in the Aquila nuclear genome. Data obtained from tissue cultures initiated from F₂ embryos of the cross Aquila x Chinese Spring suggest that at least two complementary genes are involved in this control. In contrast, the presence of new molecular arrangements appears to be under the control of a dominant allelic form of a Chinese Spring gene or genes. Thus, this study demonstrates that at least two sets of nuclear genes control the reorganization of the mitochondrial genome which occurs when tissue cultures are initiated from the immature embryos of wheat.     

Genes for ribosomal proteins S3, L16, L5 and S14 are clustered in the mitochondrial genome of Brassica napus L.

A PCR-based technique, involving the random amplification of polymorphic DNA (RAPD), was used for assessing genomic variability among a wide range of culture collection strains of black Aspergilli and related species. The performance of this technique is compared with that of the two other genetic techniques most commonly used, namely restriction fragment length polymorphisms on rDNA and isozyme analysis. The eight main groups as assigned by RFLP were also distinguished by RAPD patterns. On the basis of 122 polymorphic RAPD products using six random primers, the 17 collection strains examined could be subdivided into 15 distinct sub-groups. We suggest that the RAPD method is a quick and reliable tool for establishing the amount of genetic variability in closely related species. Our study indicates that the complex group of black Aspergilli is characterized by a high degree of genetic differentiation. This is also apparent from the considerable karyotype variation present in the group.     

The gene for the large (16S) ribosomal RNA from the Locusta migratoria mitochondrial genome

Summary The nucleotide sequence of a segment of the mtDNA molecule of the locust Locusta migratoria containing the complete large rRNA (16S) gene and some nucleotides in its vincinity has been determined. The gene contains 1314 nucleotides, comprising the smallest metazoan gene reported to date. The gene has a low content of GC (21%) and exhibits an extended sequence homology to the corresponding gene of the dipteran insect Drosophila yakuba, suggesting a comparable secondary structure. The gene structure is discussed in an evolutionary and functional context.     

Evidence for a direct relationship between mitochondrial genome organization and regeneration ability in hexaploid wheat somatic tissue cultures

Summary Embryogenic and non-embryogenic long-term callus cultures of hexaploid wheat exhibit differences in the organization of their mitochondrial genome. Embryogenic and non-embryogenic fractions of callus cultures initiated from immature embryos of the wheat cultivar Chinese Spring have been isolated and subsequently subcultured. DNA-DNA hybridization experiments using labelled cloned wheat mitochondrial DNA fragments have shown that the mitochondrial DNA organization of embryogenic subcultures derived from embryogenic parts of Chinese Spring calli is closely related to that of the initial Chinese Spring calli, while non-embryogenic subcultures derived from non-embryogenic fragments of Chinese Spring calli exhibit a mitochondrial DNA organization similar to that found in non-embryogenic calli derived from cultivar Aquila. In addition, somatic tissue cultures initiated from three other non-embryogenic wheat cultivars (Talent, Thésée and Capitole) display mitochondrial DNA arrangements similar to those found in cultivar Aquila. These results strongly suggest that, in wheat callus cultures, a particular mitochondrial genome organization is correlated with the ability of cultured cells to regenerate whole plants.Abbreviations mtDNA mitochondrial DNA - ctDNA chloroplast DNA - rRNA ribosomal RNA - kb kilobase pair - cv cultivar - 2,4-D 2,4-dichlorophenoxyacetic acid     

Organization and nucleotide sequence of ribosomal RNA genes on a circular 73 kbp DNA from the colourless flagellate Astasia longa

Summary Three tandemly arranged repeats (A, B, C) of 16S and 23S rDNA, and one supplementary (S) 16S rDNA adjacent to the 16S rDNA of repeat A, are present within an 18 kbp segment of a circular 73 kbp DNA from the colourless flagellate Astasia longa. The repeat units are separated by a short region containing a 5S rRNA gene and a gene for tRNA-Val (UAC). Sequence comparisons reveal 78%, 81%, and 67% identical nucleotides of the 23S rDNA (A), the 16S rDNA (B), and the 5S rDNA (A), respectively, with the corresponding genes of the Euglena gracilis chloroplast genome. As in Euglena chloroplasts, the 3-terminal protion of the 23S rDNA is homologous to the 4.5S rRNA gene of higher plant chloroplast genomes. These results are supportive of a common evolutionary origin for the Astasia 73 kbp DNA and the Euglena 145 kbp chloroplast DNA.     

Wheat mitochondrial 26S ribosomal RNA gene has no intron and is present in multiple copies arising by recombination

Summary Analysis of cloned SalI fragments coding for the 26S rRNA in wheat mitochondria (Triticumaestivum L.) shows that the 26S gene is contained within the same basic structural unit RS (which is about 6.6 kbp long). This repeated sequence is flanked by four different sequences I, II, III, IV in the orientations: I-RS-III, I-RS-IV, II-RS-III and II-RS-IV. This organization of the 26S gene, similar to the organization found for the 5S and 18S gene, suggests again that reciprocal intra-and/or intermolecular recombination occurs within these repeated sequences. S1 mapping and R loop mapping indicate that the 26S gene is about 3.5 kbp and has no intron.     

Organization of ribosomal RNA genes in the fungus Cochliobolus heterostrophus

Summary The genes encoding the 17S, 5.8S and 25S ribosomal RNAs in the Ascomycete Cochliobolus heterostrophus were cloned and analyzed. They are arranged in tandemly repeated units (rDNA) either 9.0 or 9.15 kilobases in length, depending upon the strain. The 5S rRNA genes are not part of the tandemly repeated rDNA. Instead, many and perhaps all of the 5S genes are dispersed in the genome, as they are in the fungi Neurospora, Aspergillus and Schizosaccharomyces. Comparative restriction maps of the rDNA from C. heterostrophus and other filamentous fungi and yeasts are presented. A survey of rDNAs from twenty-three field isolates of C. heterostrophus collected worldwide demonstrated that each isolate has one or the other of two rDNA forms, which differ in length and in the presence or absence of at least three restriction enzyme sites. The differences are all located in spacer DNA outside the coding regions for the rRNA genes. Heterogeneity in the rDNA repeat was not observed within any single isolate. The copy number of the rRNA gene cluster in C. heterostrophus is approximately 130 per haploid genome.     

Gametocidal factor-induced structural rearrangements in rye chromosomes added to common wheat

The gametocidal factor on the Aegilops cylindrical chromosome 2C^c was used to induce and analyze the nature of chromosomal rearrangements in rye chromosomes added to wheat. For this purpose we isolated plants disomic for a given rye chromosome and monosomic for 2C^c and analyzed their progenies cytologically. Rearranged rye chromosomes were identified in 7% of the progenies and consisted of rye deficiencies (4.6%), wheat–rye dicentric and rye ring chromosomes (1.8%), and terminal translocations (0.6%). The dicentric and ring chromosomes initiated breakage–fusion–bridge cycles (BFB) that ceased within a few weeks after germination as the result of chromosome healing. Of 56 rye deficiencies identified, after backcrossing and selfing, only 33 were recovered in either homozygous or heterozygous condition covering all rye chromosomes except 7R. The low recovery rate is probably caused by the presence of multiple rearrangements induced in the wheat genome that resulted in poor plant vigor and seed set, low transmission, and an underestimation of the frequency of wheat–rye dicentric chromosomes. Genomic in-situ hybridization (GISH) analysis of the 33 recovered rye deficiencies revealed that 30 resulted from a single break in one chromosome arm followed by the loss of the segment distal to the breakpoint. Only three had a wheat segment attached distal to the breakpoint. Although some of the Gc-induced rye rearrangements were derived from BFB cycles, all of the recovered rye rearrangements were simple in structure. The healing of the broken chromosome ends was achieved either by the de-novo addition of telomeric repeats leading to deficiencies and telocentric chromosomes or by the fusion with other broken ends in the form of stable monocentric terminal translocation chromosomes. This revised version was published online in July 2006 with corrections to the Cover Date.     

The organization of mitochondrial atp6 gene region in male fertile and CMS lines of pepper (Capsicum annuum L.)

The mitochondrial atp6 gene in male fertile (N) and CMS (S) pepper has previously been compared and was found to be present in two copies (Kim et al. in J Kor Soc Hort Sci 42:121–127 2001). In the current study, these atp6 copies were amplified by an inverse PCR technique, and the coding region as well as the 5′ and 3′ flanking regions were sequenced. The atp6 copies in CMS pepper were detected as one intact gene and one pseudogene, truncated at the 3′ coding region. When the atp6 genes in pepper were compared to other plant species, pepper, potato, and petunia all possessed a sequence of 12 identical amino acids at the 3′ extended region, which was considered a hallmark of the Solanaceae family. Northern blot analysis showed differences in mRNA band patterns between CMS and restorer lines, indicating that atp6 gene is one of the candidates for CMS in pepper. GenBank accession number: DQ126682 (atp6-1 genomic sequence common to fertile and CMS pepper), DQ126681 (Fertile atp6-2 genomic sequence), DQ126680 (CMS pseudo-atp6-2 genomic sequence)     

Electron microscopic investigation of mitochondrial DNA fromChenopodium album (L.)

DNA molecules from mitochondria of whole plants and a suspension culture ofChenopodium album were prepared, by a gentle method, for analysis by electron microscopy. Mitochondrial (mt) DNA preparations from both sources contained mostly linear molecules of variable sizes (with the majority of molecules ranging from 40 to 160 kb). Open circular molecules with contour lengths corresponding to 0.3–183 kb represented 23–26% of all mtDNA molecules in the preparations from the suspension culture and 13–15% in the preparations from whole plants. More than 90% of the circular DNA was smaller than 30 kb. Virtually no size classes of the mtDNA molecules could be identified, and circular or linear molecules of the genome size (about 270 kb) were not observed. In contrast, plastid (pt) DNA preparations from the suspension culture contained linear and circular molecules falling into size classes corresponding to monomers, dimers and trimers of the chromosome. About 23% of the ptDNA molecules were circular. DNA preparations from mitochondria contained a higher percentage of more complex molecules (rosette-like structures, catenate-like molecules) than preparations of ptDNA. Sigma-like molecules (putative intermediates of rollingcircle replication) were observed in mtDNA preparations from the suspension culture (18% of the circles), and in much lower amount (1%) in preparations from whole plants. The results are compared with data obtained previously by pulsed-field gel electrophoresis and discussed in relation to the structural organization and replication of the mt genome of higher plants.