Satellite DNA evolution

Satellite DNAs represent the most abundant fraction of repetitive sequences in genomes of almost all eukaryotic species. Long arrays of satellite DNA monomers form densely packed heterochromatic genome compartments and also span over the functionally important centromere locus. Many specific features can be ascribed to the evolution of tandemly repeated genomic components. This chapter focuses on the structural and evolutionary dynamics of satellite DNAs and the potential molecular mechanisms responsible for rapid changes of the genomic areas they constitute. Monomer sequences of a satellite DNA evolve concertedly through a process of molecular drive in which mutations are homogenized in a genome and fixed in a population. This process results in divergence of satellite sequences in reproductively isolated groups of organisms. However, some satellite DNA sequences are conserved over long evolutionary periods. Since many satellite DNAs exist in a genome, the evolution of species-specific satellite DNA composition can be directed by copy number changes within a library of satellite sequences common for a group of species. There are 2 important features of these satellite DNAs: long time sequence conservation and, at the same time, proneness to rapid changes through copy number alterations. Sequence conservation may be enhanced by constraints such as those imposed on functional motifs and/or architectural features of a satellite DNA molecule. Such features can limit the selection of sequences able to persist in a genome, and can direct the evolutionary course of satellite DNAs spanning the functional centromeres.

Long-term conservation vs high sequence divergence: the case of an extraordinarily old satellite DNA in bivalve mollusks

The ubiquity of satellite DNA (satDNA) sequences has raised much controversy over the abundance of divergent monomer variants and the long-time nucleotide sequence stability observed for many satDNA families. In this work, we describe the satDNA BIV160, characterized in nine species of the three main bivalve clades (Protobranchia, Pteriomorphia and Heteroconchia). BIV160 monomers are similar in repeat size and nucleotide sequence to satDNAs described earlier in oysters and in the clam Donax trunculus. The broad distribution of BIV160 satDNA indicates that similar variants existed in the ancestral bivalve species that lived about 540 million years ago; this makes BIV160 the most ancient satDNA described so far. In the species examined, monomer variants are distributed in quite a complex pattern. This pattern includes (i) species characterized by a specific group of variants, (ii) species that share distinct group(s) of variants and (iii) species with both specific and shared types. The evolutionary scenario suggested by these data reconciles sequence uniformity in homogenization-maintained satDNA arrays with the genomic richness of divergent monomer variants formed by diversification of the same ancestral satDNA sequence. Diversified repeats can continue to evolve in a non-concerted manner and behave as independent amplification-contraction units in the framework of a 'library of satDNA variants' representing a permanent source of monomers that can be amplified into novel homogeneous satDNA arrays. On the whole, diversification of satDNA monomers and copy number fluctuations provide a highly dynamic genomic environment able to form and displace satDNA sequence variants rapidly in evolution.

A GC-rich satellite DNA and karyology of the bivalve mollusk Donax trunculus: a dominance of GC-rich heterochromatin

We characterized the DTF2 satellite DNA family of the clam Donaxtrunculus and compared its chromosomal localization with cytogenetic data revealed by fluorochrome banding, C-banding, and 28S rDNA FISH. In contrast to the other satellites detected previously in this species, DTF2 is an abundant (2%) GC-rich satellite that exhibits CpG methylation. Sequence characteristics of DTF2 indicate that its evolution is not affected by constraints that might indicate some functional interactions. Fluorescence in situ hybridization revealed subtelomeric location of this satellite on a subset of 14 out of 19 D. trunculus chromosome pairs. The chromomycin A(3) (CMA) staining of GC-rich regions on D. trunculus chromosomes revealed a complex banding pattern that overlaps completely with C-bands. In total, only three bands show subtelomeric location, while 13 bands are located interstitially, one of them being coincident with the 28S rDNA hybridization signal. No bands, either CMA positive (GC-rich) or DAPI positive (AT-rich) were detected at centromeric chromosomal positions. Only two of the CMA-positive bands co-localize with the DTF2 satellite, showing a) the presence of small islands of GC-rich repetitive sequences that remained undetected by CMA/C-banding and b) the abundance of DTF2-divergent GC-rich sequences at interstitial chromosomal locations.

Complex structural features of satellite DNA sequences in the genus Pimelia (Coleoptera: Tenebrionidae): random differential amplification from a common 'satellite DNA library'

The major satellites of the nine species of the subgenera Pimelia s. str. and Amblyptera characterised in this paper are composed of longer monomers (500 and 700 bp) than those described previously in 26 Pimelia s. str. taxa (357 bp, a sequence called PIM357). Sequence analysis reveals partial similarity among these satellites and with the PIM357 monomers. The discrepancy between the phylogeny obtained based on three mitochondrial and two nuclear markers and that deduced from satellite DNA (stDNA) sequences suggests that the different Pimelia satellites were already present in a common ancestor forming what has been called a 'satellite DNA library'. Thus, the satellite profiles in the living species result from a random amplification of sequences from that 'library' during diversification of the species. However, species-specific turnover in the sequences has occurred at different rates. They have included abrupt replacements, a gradual divergence and, in other cases, no apparent change in sequence composition over a considerable evolutionary time. The results also suggest a common evolutionary origin of all these Pimelia satellite sequences, involving several rearrangements. We propose that the repeat unit of about 500 bp has originated from the insertion of a DNA fragment of 141 bp into the PIM357 unit. The 705-bp repeats have originated from a 32-bp direct duplication and the insertion of a 141-bp fragment in inverted orientation relative to a basic structure of 533 bp.

Uniform distribution of satellite DNA variants on the chromosomes of tenebrionid species Alphitobius diaperinus and Tenebrio molitor

The chromosomes of tenebrionid species Alphitobius diaperinus contain large blocks of pericentromerically located constitutive heterochromatin, as revealed by C-banding procedure. As previously reported, satellite DNA of this species is composed of two related monomeric units organized in three satellite subfamilies. In order to analyze the chromosomal location of the satellite DNA and the distribution of monomeric variants within it, and compare it with the distribution of monomer variants in Tenebrio molitor satellite DNA, the methods of in situ hybridization and restriction enzyme/nick translation were performed. Fluorescent in situ hybridization with the entire satellite DNA reveals the pericentromerically located signals on all chromosomes of the complement, coinciding with heterochromatic blocks. Results of fluorescent in situ hybridization with particular monomeric variants and of in situ restriction enzyme/nick translation show that monomeric variants are homogeneously dispersed within the entire satellite DNA. The spreading of satellite monomeric variants of the related species T. molitor within the pericentromeric heterochromatin of the entire complement, is demonstrated using the method of in situ restriction enzyme/nick translation. Although the complexity of organization of satellite DNAs is quite distinct in these two species, obtained results suggest similar efficiency of mechanisms of spreading and homogenization resulting in random chromosomal distribution of their satellite variants.

A novel interspersed type of organization of satellite DNAs in Tribolium madens heterochromatin

Analysis of arrangement of satellite DNA sequences in Tribolium madens (Insecta, Coleoptera) by Southern analysis of pulsed-field blots and two colour FISH on extended chromosomes and DNA fibres revealed a novel type of heterochromatin organization. Two satellite DNAs, distributed over the whole pericentromeric heterochromatin of all chromosomes form clusters, ranging in size from 150 kb up to several Mb. Within the clusters, both satellites are in the form of highly interspersed, short homogeneous arrays which vary in size with a lowest length limit of only few kb. The longest arrays composed of a single satellite are relatively short, up to 70 kb for satellite I, and up to 45 kb for satellite II. Only a small fraction of about 15% of satellite II is organized in long tandem repeats, while the rest is in the form of only a few repeats intermingled with satellite I. The results indicate that large clusters composed of interspersed arrays of both satellites represent a major component of T. madens heterochromatin, which is mostly devoid of long regions of other sequences. The same organizational pattern probably also includes a region of the functional centromere. We propose that such an organizational pattern of DNA sequences in heterochromatin might be common in genomes characterized by a high rate of interchromosomal exchange. This pattern of organization is different from that in other animal as well as plant species analysed up to now, in which every satellite in heterochromatin is organized in a small number of large separate domains.

Comparative study of satellite sequences and phylogeny of five species from the genus Palorus (Insecta, Coleoptera)

Major satellite sequences are analysed in the three tenebrionid beetles Palorus cerylonoides, P. genalis, and P. ficicola, and compared with the ones from P. ratzeburgii and P. subdepressus reported elsewhere. All of them are A+T rich, pericentromerically located, and with lengths of about 150 bp, either in the form of monomers or formed by more complex repeating units. A preliminary phylogenetic analysis of Palorus species using the 3' end of the mitochondrial Cytochrome Oxidase I gene shows that the five Palorus species have been diverging for a considerable amount of evolutionary time, with the pair P. ratzeburgii and P. genalis being the most closely related. Only these two taxa showed some similarity between their respective high-copy-number satellite sequences, while other satellites are mutually unrelated and might have originated independently. However, all the satellites have in common tertiary structure induced by intrinsic DNA curvature, a characteristic which is conserved within the genus. Palorus major satellites were previously detected in the genomes of congeneric species as low-copy-number clusters (Mestrović et al., Mol. Biol. Evol. 15: 1062-1068. 1998). Given the divergences between the analysed species, the substitution rate deduced from high- and low-copy-number repeats is unexpectedly low. The presence of sequence-induced DNA curvature in all Palorus satellites and similar satellite DNAs in the species pair P. ratzeburgii and P. genalis suggest (i) that constraints are at the tertiary structure; and (ii) that the satellite DNA evolutionary turnover can be dependent on the history of the taxa under study, resulting in retention of similar satellites in related taxa.

Evolution of satellite DNAs from the genus Palorus--experimental evidence for the "library" hypothesis

Satellite DNA profiles have been characterized in the congeneric species Palorus ratzeburgii, Palorus subdepressus, Palorus genalis, and Palorus ficicola (Coleoptera, Insecta), each of which contains a single, A + T-rich satellite DNA comprising a considerable portion of the genome (20%-40%). These satellites exhibit insignificant mutual sequence similarity. Using PCR assay, it has been shown that all four sequences are present in each of the tested Palorus species: one of them is amplified into a high copy number or a major satellite, while the three others are in the form of low-copy-number repeats estimated to make up approximately 0.05% of the genome. Each of the four satellites is interspecifically high conserved concerning the sequence, monomer length, and tandem repeat organization. Major, as well as low-copy-number, satellites are colocalized in the regions of pericentromeric heterochromatin on all chromosomes of the complement. The low-copy-number satellites are dispersed between the large arrays of the major satellite over the whole heterochromatic block. Our results explain satellite DNA evolution, confirming the hypothesis that related species share a "library" of conserved satellite sequences, some of which could be amplified into a major satellite. Due to the evolutionary dynamics of satellite DNAs, the content of the "library" is variable; the elimination of some sequences parallels the creation of the new ones. Quantitative changes in satellite DNAs, induced by occasional amplification of satellite repeat from the "library", could possibly occur in the course of the speciation process, thus forming a species-specific profile of satellite DNAs.

Similarity of structural features and evolution of satellite DNAs from palorus subdepressus (Coleoptera) and related species

A novel highly abundant satellite DNA comprising 20% of the genome has been characterized in Palorus subdepressus (Insecta, Coleoptera). The 72-bp-long monomer sequence is composed of two copies of T2A5T octanucleotide alternating with 22-nucleotide-long elements of an inverted repeat. Phylogenetic analysis revealed clustering of monomer sequence variants into two clades. Two types of variants are prevalently organized in an alternating pattern, thus showing a tendency to generate a new complex repeating unit 144 bp in length. Fluorescent in situ hybridization revealed even distribution of the satellite in the region of pericentric heterochromatin of all 20 chromosomes. P. subdepressus satellite sequence is clearly species specific, lacking similarity even with the satellite from congeneric species P. ratzeburgii. However, on the basis of similarity in predicted tertiary structure induced by intrinsic DNA curvature and in repeat length, P. subdepressus satellite can be classified into the same group with satellites from related tenebrionid species P. ratzeburgii, Tenebrio molitor, and T. obscurus. It can be reasonably inferred that repetitive sequences of different origin evolve under constraints to adopt and conserve particular features. Obtained results suggest that the higher-order structure and repeat length, but not the nucleotide sequence itself, are maintained through evolution of these species.

Conservation of satellite DNA in species of the genus Pimelia (Tenebrionidae, Coleoptera)

Satellite DNA has been characterized in six allopatric species from the genus Pimelia: P. interjecta, P. integra, P. variolosa and P. baetica, inhabiting Iberian Peninsula, and P. elevata and P. criba, endemic to Balearic Islands Ibiza and Mallorca, respectively. All species show the presence of a single satellite DNA of a basic monomer length of 357 bp and A+T content of 69%, comprising a considerable amount of the genome (39%-45%, corresponding to about 4.5 x 10(5) copies per haploid genome). The sequence analysis of 22 cloned repeats reveals very high intra- and interspecific sequence similarity. Phylogenetic analysis separates the satellite sequences into two clusters, each comprising clones from three species exclusively. Within the clusters, satellite clones are not grouped species-specifically, except those of P. integra where species-diagnostic nt substitutions are detected with a pattern that could be produced by gene conversion. Such high sequence conservation could be related to preservation of satellite DNA curvature, resulting in a higher order helical structure, proposed to act as a specific protein binding domain.

Characterization of interrelated sequence motifs in four satellite DNAs and their distribution in the genome of the mollusc Donax trunculus

A family of four satellite DNAs has been characterized in the genome of the bivalve mollusc, Donax trunculus. All share HindIII sites, a similar monomer length of about 160 base pairs (bp), and the related oligonucleotide motifs GGTCA and GGGTTA, repeated six to 15 times within the repetitive units. The motif GGTCA is common to all members of the satellite family. It is present in three of them in both orientations, interspersed within nonrepetitive DNA sequences. The hexanucleotide GGGTTA appears to be the main building element of one of the satellites forming a prominent subrepeat structure in conjunction with the 5-bp motif. The former has been also found in perfect tandem repeats in a junction region adjacent to the proper satellite sequence. Southern analysis has revealed that (GGGTTA)n and/or related sequences are abundant and widely distributed in the D. trunculus genome. The distribution observed is consistent with the concurrence of the scattering of short sequence motifs throughout the genome and the spread of longer DNA segments, with concomitant formation of satellite monomer repeats. Both kinds of dispersion may have contributed to the observed complex arrangement of the HindIII satellite DNA family in Donax.

Satellite DNA of the red flour beetle Tribolium castaneum--comparative study of satellites from the genus Tribolium

A highly abundant satellite DNA comprising 17% of the Tribolium castaneum (Insecta, Coleoptera) genome was cloned and sequenced. The satellite monomer is 360 bp long, has a high A+T content of 73%, and lacks significant internal substructures. The sequence variability is 3.6%, essentially due to random distribution of single-point mutations. The satellite is evenly distributed in the regions of centromeric heterochromatin of all 20 chromosomes, as shown by fluorescent in situ hybridization. Comparison of T. castaneum satellite with those from three different but congeneric species reveals the highest sequence similarity of 47.1% with the satellite from the sibling species Tribolium freemani. The phylogenetic relationships among Tribolium species deduced from satellite sequence agree with those based on karyological, chemotaxonomic, and hybridization data. This indicates a parallel in the divergence of satellites and some genetic and cytogenetic characters. Despite low mutual sequence similarity, which makes them species-specific, Tribolium satellites have a common structural characteristic: a block of about 95% A+T content, 20 to 42 bp long, flanked at one side by an inverted repeat which can potentially form a thermodynamically stable dyad structure. Since similar structural features are found in centromeric DNA of Saccharomyces cerevisiae and Chironomus pallidivittatus, their possible importance in centromere function may be inferred.

Characterization of a complex satellite DNA in the mollusc Donax trunculus: analysis of sequence variations and divergence

A highly repetitive sequence in the genomic DNA of the bivalve mollusc Donax trunculus (Dt) has been identified upon restriction with EcoRV. During the time-course of DNA digestion, genomic fragments resolved electrophoretically into a ladder-like banding pattern revealing a tandem arrangement of the repeated elements, thus representing satellite DNA sequences. Cloning and sequence analysis unraveled the presence of two groups of monomer units which can be considered distinctive satellite subfamilies. Each subclass is distinguishable by the presence of 17 evenly spread diagnostic nucleotides (nt). The respective consensus sequences are 155 bp in length and differ by 11%, while relevant internal substructures were not observed. The two satellite subfamilies constitute 0.23 and 0.09% of the Dt genome, corresponding to 20 000 and 7600 copies per haploid complement, respectively. Sequence mutations often appear to be shared between two or more monomer variants, indicating a high degree of homogenization as opposed to that of random mutational events. Shared mutations among variants appear either as single changes or in long stretches. This pattern may arise from gene conversion mechanisms acting at different levels, such as the spread of nt sequences of a similar length to the monomer repeat itself, and the diffusion of short tracts a few bp long. Subfamilies might have evolved from the occasional amplification and spreading of a monomer variant effected by gene conversion events.

Evolution of Tribolium madens (Insecta, Coleoptera) satellite DNA through DNA inversion and insertion

Two different satellite DNAs from tenebrionid species Tribolium madens (Insecta, Coleoptera) have been detected, cloned, and sequenced. Satellite I comprises 30% of the genome; it has a monomer size of 225 bp and a high A + T content of 74%. Satellite II, with a monomer size of 711 bp and A + T content of 70%, is less abundant, making 4% of the total DNA. Sequence variability of the monomers relative to consensus sequence is 4.1% and 1.2% for satellite I and II, respectively. Both satellites are localized in the heterochromatic regions of all chromosomes. A search for internal motifs showed that both satellites contain a related subsequences, about 100 bp long. The creation of satellite I monomer is explained by duplication of the basic subunit, followed by subsequent divergence by single point mutations, deletions, and gene conversion. Inversion of the subsequence in addition to its duplication has occurred in satellite II. The result of this inversion is possible formation of a long, stable dyad structure. The 408-bp sequence, inserted within satellite II monomer, shares no similarity with a basic subunit. Frequent direct repeats found within the inserted sequence point to its evolution by duplication of shorter motifs. It is proposed that both satellites have been derived from a common ancestral sequence whose duplication played a major role in the formation of satellite I monomer, while insertion of a new sequence together with inversion of an ancestral one induced the occurrence of satellite II.

Characterization of two abundant satellite DNAs from the mealworm Tenebrio obscurus

Two highly abundant satellite DNAs comprise 36% of the Tenebrio obscurus (Tenebrionidae, Coleoptera) genome. They are designated as satellite I and satellite II with the monomer length of 344 and 142 base pairs (bp), respectively. Both satellites differ in their nucleotide (nt) sequences, but the frequency of point mutations, well-conserved length of monomer variants, stretches of shared mutations characteristic for the process of gene conversion, and distribution of both satellites in regions of centromeric heterochromatin of all chromosomes indicate that the same evolutionary processes act on both of them with the same, or similar, rate. While satellite I shares no sequence similarity with any other known nt sequence, satellite II is 79.7% homologous with the highly abundant satellite from closely related Tenebrio molitor. Difference in the frequency of point mutations and absence of shared mutations indicating gene conversion strongly suggest that in these two closely related species mutational processes affecting satellite DNAs seem to be changed. Retarded electrophoretic mobility, due to sequence-induced curvature of DNA helix axis, was observed for T. obscurus satellite II, but not for satellite I. Although evolutionary processes act with different rates in T. obscurus and T. molitor satellites the monomer length and sequence-induced curvature are well preserved in both 142-bp satellites, as well as in, at the nt sequence level completely divergent, Palorus ratzeburgii (Tenebrionidae) satellite, indicating potential importance of these parameters in their evolution.

Tandemly repeated pentanucleotides in DNA sequences of eucaryotes

Genetic sequence data banks were scanned in order to retrieve tandemly repeated pentanucleotides (pnts). It was found that among 102 (=(1024-4)/2/5) possible distinct pnts roughly each fourth is involved in tandem repeats. It is shown that tandemly repeated pnts are composed of frequently occurring di- and trinucleotides and that those pnts which occur frequently in the form of mono- or di-pnts form also tandem repeats either in the form of satellites or in the form of shorter tandem repeats. Human satellite III is taken as a specific example. It is shown that the first guanine within GG-AAT pnt exhibits the highest mutability. Sequential distribution of base changes gives evidence that the mutations do not occur at random positions but in a correlated fashion so that long stretches of original pnts remain intact. It is found that pnts related to the satellite III are present in introns and flanking regions of some structural genes, but are not preserved between orthologous genes of related species. The results corroborate the most plausible mechanism of their evolution--rapid amplification followed by successive divergence of repeat units by various mutational processes.

Tenebrio obscurus satellite DNA is resistant to cleavage by restriction endonucleases in situ

Satellite DNA from the mealworm beetle, Tenebrio obscurus, is composed of 344 bp long monomers of high AT content (68%), and represents 15% of the total DNA. In situ hybridization reveals the positions of the satellite on the pericentromeric heterochromatin of all T. obscurus chromosomes. To compare restriction enzyme (RE) effects with those on naked DNA, fixed chromosomes were digested with REs having recognition sites in most of the satellite monomers, and also with enzymes having target sites present only partially, or very rarely in the satellite units. All enzymes produce similar C-like banding patterns showing heterochromatin resistance to digestion regardless of the enzyme used. In situ nick translation suggests the inability of REs to cleave satellite DNA rather than the inefficient extraction of DNA fragments. DNA in heterochromatin was only extensively digested when the chromosomes were preincubated with proteinase K, indicating that accessibility of REs to DNA is increased by the removal of chromosomal proteins. This is in contrast to recently obtained results in Tenebrio molitor, where cleavage of satellite DNA is equally efficient in both fixed chromosomes and in naked DNA. The satellite DNAs of the two congeneric species differ in their AT content, and their primary and higher order structure, which could influence both heterochromatin structure and the accessibility of REs to satellite DNA.

Analysis of divergence of Alphitobius diaperinus satellite DNA--roles of recombination, replication slippage and gene conversion

Satellite DNA is highly abundant in Alphitobius diaperinus (Tenebrionidae, Coleoptera), comprising 25% of the total genomic DNA. Sequence analysis reveals an average GC content of 50.8% and the presence of three different groups of satellite monomer variants, tH1, tH2 and tH3 with corresponding lengths of 123, 128 and 126 bp. Their mutual homologies range between 65 and 81%. Sequence comparison shows that the monomer variant tH2 has been formed by a recombination process between tH1 and tH3, which have a low average homology of only 65.15%. The longest stretch of 100% homology between the recombining units is 17 bp and is located 3' to the predicted recombination site. There is also an indication from sequence analysis that replication slippage and gene conversion play a part in the formation of satellite units and contribute to their divergence. The tH1, tH2 and tH3 monomer variants are organized in higher order repeating structures: a dimer, composed of tH1 and tH3, and a trimer containing tH1, tH2 and tH3 in series. The dimeric and trimeric repeat units furthermore create three higher order satellite subfamilies. Two of them contain either tandemly arranged dimers or trimers, while the third one is composed of both types of repeats, mutually interspersed.

Satellite DNA and heterochromatin of the flour beetle Tribolium confusum

The chromosomes of Tribolium confusum have conspicuous bulks of pericentromeric constitutive heterochromatin. The amount of heterochromatin measured by C-banding in metaphase chromosomes is estimated to be 40-45%. It is composed of an A + T rich DNA according to the distamycin A/diamidinophenylindol staining of chromosomes. Restriction analysis of isolated T. confusum genomic DNA shows that this species has a satellite DNA that constitutes about 40% of the genome. Cloning and sequencing experiments reveal a monomer length of 158 base pairs and a copy number of 5.77 x 10(5) per haploid genome. Its sequence is A + T rich (73%), with direct and inverted repeats, one of them with a possibility of forming stable cruciform structure. The abundance, monomer length, and the mutation rate are similar to those found in other satellite families from different species of Tenebrionidae, but no sequence homology has been found among them. No retarded mobility of satellite DNA, characteristic for molecules with sequence-induced curvature, has been detected by electrophoresis on nondenaturing polyacrylamide gels. In situ digestions with restriction enzymes and in situ hybridization show that this satellite DNA is located in pericentromeric positions of all chromosomes coinciding with C-bands.

Detection of satellite DNA in Palorus ratzeburgii: analysis of curvature profiles and comparison with Tenebrio molitor satellite DNA

Very abundant and homogenous satellite DNA has been found in the flour beetle Palorus ratzeburgii, representing 40% of its genome. Sequencing of 14 randomly cloned satellite monomers revealed a conserved monomer length of 142 bp and an average A+T content of 68%. Sequence variation analysis showed that base substitutions, appearing with a frequency of 2.3%, are predominant differences among satellite monomers. The satellite sequence is unique without significant direct repeats and with only two potentially stable inverted repeats. After electrophoresis of satellite monomers on native polyacrylamide gel retarded mobilities characteristic for curved DNA molecules are observed. The curvature profiles and DNA helix axis trajectory are calculated on the basis of three different algorithms. These calculations predict that P ratzeburgii satellite DNA forms a left-handed solenoid superstructure. Comparison of described features with other satellite DNAs reveals some striking similarities with satellite DNA from related species Tenebrio molitor, which belongs to the same family of Tenebrionidae. Both satellites are very abundant and homogenous with the same, highly conserved monomer length, although there is no homology at the nucleotide level. Their monomers, as well as multimers, exhibit very similar retarded electrophoretic mobilities. The calculated curvature profiles predict two bend centers in monomers of each satellite, resulting in a model of left-handed solenoid superstructures of similar appearance.

Evidence for random distribution of sequence variants in Tenebrio molitor satellite DNA

Tenebrio molitor satellite DNA has been analysed in order to study sequential organization of tandemly repeated monomers, i.e. to see whether different monomer variants are distributed randomly over the whole satellite, or clustered locally. Analysed sequence variants are products of single base substitutions in a consensus satellite sequence, producing additional restriction sites. The ladder of satellite multimers obtained after digestion with restriction enzymes was compared with theoretical calculations and revealed the distribution pattern of particular monomer variants within the satellite. A defined higher order repeating structure, indicating the existence of satellite subfamilies, could not be observed. Our results show that some sequence variants are very abundant, being present in nearly 50% of the monomers, while others are very rare (0-1% of monomers). However, the distribution of either very frequent, or very rare sequence variants in T. molitor satellite DNA is always random. Monomer variants are randomly distributed in the total satellite DNA and thus spread across all chromosomes, indicating a relatively high rate of sequence homogenization among different chromosomes. Such a distribution of monomer variants represents a transient stage in the process of sequence homogenization, indicating the high rate of spreading in comparison with the rate of sequence variant amplification.

Sequence of the 5S rRNA gene and organization of ribosomal RNA operons in Streptomyces rimosus

One Streptomyces rimosus ribosomal RNA gene set (rrnF) was cloned into pBR322 as 8.8 kilobase-pairs BamHI fragment and sequence of the 3' end of the operon with 5S rRNA gene was determined. 5S rRNA gene is 120 bp long and highly homologous with two other known 5S rRNA from Streptomyces. Remarkable sequence homology with S. ambofaciens rrnD operon exists in the 3' noncoding regions, including first transcription termination signal. S. rimosus rrnF operon contains second putative terminator which is absent in S. ambofaciens rrnD operon. tRNA genes were not found at the 3' end of rrnF operon. The number of rRNA operons in S. rimosus was defined by Southern hybridization analysis. S. rimosus possess six rRNA operons and all rRNA operons contain identical PstI fragment of 4.5 kb. rRNA genes in operons are separated by short intergenic regions and organized in the order 16S-23S-5S. Efforts to connect tRNA genes with S. rimosus rRNA operons were unsuccessful.

Sequence-induced curvature of Tenebrio molitor satellite DNA

Single satellite DNA constitutes about 50% of the Tenebrio molitor genome. Electrophoresis of 142 base pair long satellite monomers on nondenaturating polyacrylamide gel shows retarded mobility, a characteristic of fragments with sequence-induced DNA curvature. Migrational analysis of circularly permuted satellite monomers revealed the existence of 2 bend centers in the monomer sequence. We calculated the trajectory of DNA helix axis according to the algorithm of De Santis et al. This model predicts that T molitor naked satellite DNA forms a solenoid structure with left-handed superhelix. One turn of the superhelix has approximately 310 base pairs and a 33 nm pitch. Point mutations found in the satellite DNA (1.8%) influence bending characteristics, but do not distort the general geometry of satellite superhelix.

Five transfer RNA genes lacking CCA termini are clustered in the chromosome of Streptomyces rimosus

The nucleotide sequence of a 1105 bp Streptomyces rimosus DNA fragment containing five transfer RNA genes was determined. Two tRNA(Gln) (CUG) genes, differing by 1 bp in the aminoacyl stem, and three identical tRNA(Glu) (CUC) genes were identified. The five tRNA genes, arranged in the order: Gln1-Glu1-Glu2-Gln2-Glu3, were separated by short, nonhomologous intergenic regions. Surprisingly, none of these tRNA genes encoded the CCA 3' terminus of mature tRNAs. All five encoded tRNAs for the translation of GC rich codons, which are preferentially used in Streptomyces genes (CAG and GAG, respectively). We recently reported nucleotide sequences of two initiator tRNA genes from S. rimosus, which also do not encode the CCA end of mature tRNAs. It is therefore very likely that S. rimosus represents an example of those eubacteria in which the majority of tRNA genes do not encode the 3' terminal CCA end of mature tRNAs. Evolutionary implications of this finding remain to be elucidated.

Sequence variability of satellite DNA from the mealworm Tenebrio molitor

To determine the consensus sequence of a 142-bp-long satellite monomer from the mealworm Tenebrio molitor, 22 clones were sequenced. Only nucleotide (nt) substitutions were found. The average sequence variability is 2.5 nt per monomer; changes are predominantly C----T and G----A transitions and the sequence tends to become A + T-rich. T. molitor satellite DNA is undermethylated and transcriptionally inactive.

Effects of spermine and magnesium ions on the aminoacylation of yeast tRNA(Tyr)

Stimulatory effects of Mg2+ and spermine on the kinetics of the aminoacylation of tRNA(Tyr) were examined using purified yeast tRNA(Tyr) and tyrosyl-tRNA synthetase. The apparent Km for tRNA(Tyr) was the lowest at Mg2+ concentrations between 2 and 5 mM and was not influenced by spermine. In the absence of spermine, the apparent Vmax was the highest at Mg2+ concentrations of 5 mM or higher, whereas the presence of spermine strongly stimulated the reaction at lower Mg2+ concentrations. Spermine alone could not substitute for Mg2+, nor was it able, at any Mg2+ concentration, to increase the reaction rate above the level reached at high concentrations of Mg2+ alone. Calculations of the concentration of Mg3.tRNA(Tyr) complex as a function of initial Mg2+ concentration, using the binding constants derived from physical measurements, allow the conclusion that spermine exerts its stimulatory activity by creating strong binding sites for Mg2+; this would enable the tRNA to assume the conformation required for optimal aminoacylation. The conformational requirement for the first tRNA: synthetase encounter is obviously less stringent, since the apparent Km for tRNA(Tyr) is not influenced by spermine.