Expansion and Evolution of the X-Linked Testis Specific Multigene Families in the melanogaster Species Subgroup

The testis specific X-linked genes whose evolution is traced here in the melanogaster species subgroup are thought to undergo fast rate of diversification. The CK2ßtes and NACβtes gene families encode the diverged regulatory β-subunits of protein kinase CK2 and the homologs of β-subunit of nascent peptide associated complex, respectively. We annotated the CK2βtes-like genes related to CK2ßtes family in the D. simulans and D. sechellia genomes. The ancestor CK2βtes-like genes preserved in D. simulans and D. sechellia are considered to be intermediates in the emergence of the D. melanogaster specific Stellate genes related to the CK2ßtes family. The CK2ßtes-like genes are more similar to the unique autosomal CK2ßtes gene than to Stellates, taking into account their peculiarities of polymorphism. The formation of a variant the CK2ßtes gene Stellate in D. melanogaster as a result of illegitimate recombination between a NACßtes promoter and a distinct polymorphic variant of CK2ßtes-like ancestor copy was traced. We found a close nonrandom proximity between the dispersed defective copies of DINE-1 transposons, the members of Helitron family, and the CK2βtes and NACβtes genes, suggesting an involvement of DINE-1 elements in duplication and amplification of these genes

Molecular Evolution of Two Paralogous Tandemly Repeated Heterochromatic Gene Clusters Linked to the X and Y Chromosomes of Drosophila melanogaster

Here we report the peculiarities of molecular evolution and divergence of paralogous heterochromatic clusters of the testis- expressed X-linked Stellate and Y-linked Su(Ste) tandem repeats. It was suggested that Stellate and Su(Ste) clusters affecting male fertility are the amplified derivatives of the unique euchromatic gene βCK2tes encoding the putative testis-specific β-subunit of protein kinase CK2. The putative Su(Ste)-like evolutionary intermediate was detected on the Y chromosome as an orphon outside of the Su(Ste) cluster. The orphon shows extensive homology to the Su(Ste) repeat, but contains several Stellate-like diagnostic nucleotide substitutions, as well as a 10-bp insertion and a 3′ splice site of the first intron typical of the Stellate unit. The orphon looks like a pseudogene carrying a drastically damaged Su(Ste) open reading frame (ORF). The putative Su(Ste) ORF, as compared with the Stellate one, carries numerous synonymous substitutions leading to the major codon preference. We conclude that Su(Ste) ORFs evolved on the Y chromosome under the pressure of translational selection. Direct sequencing shows that the efficiency of concerted evolution between adjacent repeats is 5–10 times as high in the Stellate heterochromatic cluster on the X chromosome as that in the Y-linked Su(Ste) cluster, judging by the frequencies of nucleotide substitutions and single-nucleotide deletions

Molecular Evolution of Two Paralogous Tandemly Repeated Heterochromatic Gene Clusters Linked to the X and Y Chromosomes of Drosophila melanogaster

Here we report the peculiarities of molecular evolution and divergence of paralogous heterochromatic clusters of the testis- expressed X-linked Stellate and Y-linked Su(Ste) tandem repeats. It was suggested that Stellate and Su(Ste) clusters affecting male fertility are the amplified derivatives of the unique euchromatic gene βCK2tes encoding the putative testis-specific β-subunit of protein kinase CK2. The putative Su(Ste)-like evolutionary intermediate was detected on the Y chromosome as an orphon outside of the Su(Ste) cluster. The orphon shows extensive homology to the Su(Ste) repeat, but contains several Stellate-like diagnostic nucleotide substitutions, as well as a 10-bp insertion and a 3′ splice site of the first intron typical of the Stellate unit. The orphon looks like a pseudogene carrying a drastically damaged Su(Ste) open reading frame (ORF). The putative Su(Ste) ORF, as compared with the Stellate one, carries numerous synonymous substitutions leading to the major codon preference. We conclude that Su(Ste) ORFs evolved on the Y chromosome under the pressure of translational selection. Direct sequencing shows that the efficiency of concerted evolution between adjacent repeats is 5–10 times as high in the Stellate heterochromatic cluster on the X chromosome as that in the Y-linked Su(Ste) cluster, judging by the frequencies of nucleotide substitutions and single-nucleotide deletions

Paralogous Stellate and Su(Ste) repeats: evolution and ability to silence a reporter gene

The X-linked Stellaterepeats, encoding a putative regulatory subunit of protein kinase CK2, are expressed in XO male testes. The Y-linked, testes-expressed paralogous Su(Ste) repeats are thought to be suppressors of Stellatetranscription. The unique, testis-expressed euchromatic gene was suggested to be an ancestor of the both types of amplified paralogous repeats. A Su(Ste)-like orphon was localized on a Y chromosome, outside of the Su(Ste) cluster. Several diagnostic molecular markers peculiar for the both types of diverged Stellateand Su(Ste) units were detected in the orphon sequence. The orphon was suggested to be a close relative of the immediate ancestor of both types of paralogous repeats which initiated evolution on the Y chromosome. Selection pressure on the level of translation was shown as a driving force in the evolution of Su(Ste) repeats, which are considered as more ancient derivatives of the ancestor euchromatic gene than Stellaterepeats. In a vicinity of 12E Stellatecluster the undamaged, recently originated euchromatic Stellateorphon was found at 12D, providing the poly(A) signal for the bendlessgene. P-element mediated transformations reveal that the fragments of cloned Stellateand Su(Ste) clusters are able to induce variegation of a reporter mini-whitegene. The observed variegation phenomenon has peculiar features: a significant increase of trans-activation of a reporter mini-whitegene in homozygous stat; absence of effects of several conventional modifiers of position effect variegation (PEV) and independence of a severity of variegation on a distance between insertion and centromere region

Multiple alignment of <i>DINE-1</i>copies in syntenic regions of <i>D. melanogaster</i> and <i>D. simulans/D. sechellia</i>.

<p>(<b>A</b>) Alignment of known and novel <i>DINE-1</i> copies with <i>D. melanogaster DINE-1</i> consensus sequence (DINEYang) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Yang2" target="_blank">[26]</a>; consensus regions are designated according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Yang2" target="_blank">[26]</a>; (<b>B</b>) Alignment of the <i>simINE_ben</i> and <i>DNAREP1_DM</i> consensus sequence <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Kapitonov3" target="_blank">[36]</a>.</p

Recombination between the ancestor <i>CK2βtes</i>-<i>like</i> gene (GD15860 or GM17570) and <i>NACβtes</i> promoter region.

<p>Signature sequence of putative <i>CK2βtes</i>-like partner is designated in bold italics. The distances in nucleotides from the start of signature sequence and ORF start are indicated in brackets. Broken line shows the site of fusion of the <i>CK2βtes</i>-like and <i>NACβtes</i> sequences as a result of recombination. The tree represents the similarity of the nucleotide sequences in the selected box measured as the number of base differences <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-S1" target="_blank">[42]</a> and was constructed using the UPGMA method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037738#pone.0037738-Sneath1" target="_blank">[43]</a>. The percentage of replicate trees in which the associated sequence clustered together in the bootstrap test (500 iterations) are shown next to the branches. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed.</p

Fate of multigene families in the course of the divergence of <i>melanogaster</i> group species.

<p>Fate of multigene families in the course of the divergence of <i>melanogaster</i> group species.</p

Paralogous Stellate and Su(Ste) repeats: evolution and ability to silence a reporter gene

The X-linked Stellaterepeats, encoding a putative regulatory subunit of protein kinase CK2, are expressed in XO male testes. The Y-linked, testes-expressed paralogous Su(Ste) repeats are thought to be suppressors of Stellatetranscription. The unique, testis-expressed euchromatic gene was suggested to be an ancestor of the both types of amplified paralogous repeats. A Su(Ste)-like orphon was localized on a Y chromosome, outside of the Su(Ste) cluster. Several diagnostic molecular markers peculiar for the both types of diverged Stellateand Su(Ste) units were detected in the orphon sequence. The orphon was suggested to be a close relative of the immediate ancestor of both types of paralogous repeats which initiated evolution on the Y chromosome. Selection pressure on the level of translation was shown as a driving force in the evolution of Su(Ste) repeats, which are considered as more ancient derivatives of the ancestor euchromatic gene than Stellaterepeats. In a vicinity of 12E Stellatecluster the undamaged, recently originated euchromatic Stellateorphon was found at 12D, providing the poly(A) signal for the bendlessgene. P-element mediated transformations reveal that the fragments of cloned Stellateand Su(Ste) clusters are able to induce variegation of a reporter mini-whitegene. The observed variegation phenomenon has peculiar features: a significant increase of trans-activation of a reporter mini-whitegene in homozygous stat; absence of effects of several conventional modifiers of position effect variegation (PEV) and independence of a severity of variegation on a distance between insertion and centromere region

Eu-heterochromatic Rearrangements Induce Replication of Heterochromatic Sequences Normally Underreplicated in Polytene Chromosomes of Drosophila melanogaster

In polytene chromosomes of D. melanogaster the heterochromatic pericentric regions are underreplicated (underrepresented). In this report, we analyze the effects of eu-heterochromatic rearrangements involving a cluster of the X-linked heterochromatic (Xh) Stellate repeats on the representation of these sequences in salivary gland polytene chromosomes. The discontinuous heterochromatic Stellate cluster contains specific restriction fragments that were mapped along the distal region of Xh. We found that transposition of a fragment of the Stellate cluster into euchromatin resulted in its replication in polytene chromosomes. Interestingly, only the Stellate repeats that remain within the pericentric Xh and are close to a new eu-heterochromatic boundary were replicated, strongly suggesting the existence of a spreading effect exerted by the adjacent euchromatin. Internal rearrangements of the distal Xh did not affect Stellate polytenization. We also demonstrated trans effects exerted by heterochromatic blocks on the replication of the rearranged heterochromatin; replication of transposed Stellate sequences was suppressed by a deletion of Xh and restored by addition of Y heterochromatin. This phenomenon is discussed in light of a possible role of heterochromatic proteins in the process of heterochromatin underrepresentation in polytene chromosomes

Stellate Repeats: Targets of Silencing and Modules Causing cis-Inactivation and trans-Activation

The mechanism of silencing of testis expressed X-linked Stellate repeats by homologous Y-linked Suppressor of Stellate [Su(Ste)] repeats localized in the crystal locus was studied. The double stranded RNA as a product of symmetrical transcription of Su(Ste) repeat and small iinterfaceSu(Ste) siRNA were revealed suggesting the mechanism of RNA interference (RNAi) for Stellate silencing. The relief of Stellate silencing as a result of impaired complementarity between the sequences of putative target Stellate transcripts and Su(Ste) repeats was shown. The role of RNAi mechanism in the silencing of heterochromatic retrotransposon GATE inserted in Stellate cluster was revealed. The studies of cis-effects of Stellate tandem repeats causing variegated expression of juxtaposed reporter genes were extended and the lacZ variegation in imaginal disc was shown. The exceptional case of a non-variegated expression of mini-white gene juxtaposed to Stellate repeats in a construct inserted into the 39C region was shown to be accompanied by trans-activation in homozygous state. Trans-activation effect was retained after transposition of this construct into heterochromatic environment in spite of strong variegation of a mini-white gene