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  • 1
    Electronic Resource
    Electronic Resource
    Structural constraints in expansion segments from a midge 26S rDNA (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 1016-1021 
    Details
    ISSN: 1432-1432
    Keywords: Chironomus ; LSU rRNA evolution ; Expansion segments ; Compensatory mutations ; rRNA processing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract DNA sequences representing approximately 40% of the large-subunit rRNA gene from the lower dipteran Chironomus thummi were analyzed. Once aligned with their Drosophila counterparts, sequence and base content comparisons were carried out. Sequence identity was found to be high overall, except for six regions that displayed a local bias in nucleotide composition toward AT. These regions were identified as expansion segments D3, D4, D5, D6, D7a, and D12. Besides base sequence divergence, differences in length were observed between the respective variable domains of the two species, particularly for D7a. Prediction of secondary structure showed that the folding of the Chironomus expansion segments analyzed is in agreement with the general patterns proposed for eukaryotic LSU rRNA. The comparison with Drosophila revealed also that the Chironomus secondary structures of the variable domains are supported by multiple compensatory substitutions or even compensatory insertions. Chironomus D7a displayed an unusual structural feature with respect to the insect D7a models that have been inferred up to now. The structural constraint observed in the expansion segments of Diptera so distantly related as midges and Drosophila suggests that these regions contribute to some functional role. Concerning the D7a of insects so far analyzed, there can be, in addition to a conserved secondary structure, a nucleotide composition constraint that might be important for the process giving rise to the alpha and beta halves of the 26S rRNA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00173183
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  • 2
    Electronic Resource
    Electronic Resource
    Functional analysis of the 3′-terminal part of the Balbiani ring 2.2 gene by interspecies sequence comparison (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 221-227 
    Details
    ISSN: 1432-1432
    Keywords: Balbiani rings ; Nucleotide sequence ; 3′ ends ; Repeat units ; Evolutionary conservation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary An interspecies comparison was made between the 3′ ends of Balbiani ring genes fromChironomus. The comparison was focused on the BR2.2 gene, and a part at the 3′ end fromChironomus pallidivittatus (which included also a segment of the gene core) was cloned. Its sequence, and other previously published BR sequences from this species and fromChironomus tentans were used in the analysis. The 3′ parts of these repetitive genes can be divided into a region belonging to the core of the genes followed by a terminal region. In the core region the repeats (each of which consists of a constant part and a subrepeated part) are highly similar and the constant parts show little interspecies differentiation. Furthermore, the two parts of the repeats are units in an evolutionary and probably also functional sense. The terminal region contains modified constant units, usually isolated betwen acidic so-called cys regions, the whole arrangement lying upstream of an intron toward a 3′-terminal exon. Most of the modified constant units are mosaics in rates of evolution with stable outer quarters bordering to equally stable cys regions and a central half with a very high rate of evolution. One of the terminal units, present only in the BR2.2 gene and second from the end, differs distinctly not only from corresponding core units but also from other terminal units in the three normally active BR genes. It lies upstream of all cys regions and is evolutionarily conserved over most of its length. Furthermore, two-dimensional protein structure prediction does not exclude an endoproteolytic cleavage site in this unit. Such a site appears unlikely in other terminal or core regions. This is of interest in view of evidence for intracellular cleavage of the BR2.2 terminal region with liberation of a part containing a DNA-binding domain (Botella et al. 1988). All in all the fine anatomy of evolutionary changes at the BR gene termini shows interesting correlations with postulated functional relations and may have predictive value in the further functional analysis of this part of the gene.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02109499
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  • 3
    Electronic Resource
    Electronic Resource
    Subrepeats within the BR1β repeat unit inChironomus pallidivittatus can be classified into different types depending on codon usage (1988)
    Springer
    Journal of molecular evolution 27 (1988), S. 298-302 
    Details
    ISSN: 1432-1432
    Keywords: Balbiani rings ; cDNA clones ; Nucleotide sequence ; Repeat units ; Subrepeats
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A new type of repeat unit was isolated from Balbiani ring 1 ofChironomus pallidivittatus and designated, BR1β repeat. It consists of a constant and a subrepeated part, like previously described units belonging to the core blocks of the BR genes. The subrepeated part contains 10-codon subrepeats with an arrangement similar to the subrepeats of the previously described BR2β gene. The present unit differs from earlier reported core units firstly in a much lower number of copies (about 15) per genome, which are tandemly arranged. Secondly, the number of subrepeats per BR1β repeat unit can show great variations. On the basis of the pattern of codon usage, three types of subrepeats can be distinguished. One type lies 5′-proximal in the subrepeat array and consists of variable numbers of subrepeats almost identical at the nucleotide level. The last complete subrepeat represents another type, with consistent differences in codon usage as compared to subrepeats of the proximal type. Finally, there is an intermediate type represented by the subrepeat preceding the distal one. Here, codon characteristics from proximal and distal subrepeats are mixed in a patchy and irregular way. The evolution of the arrays can be understood either as being the result of subrepeat formation in two steps (occurring before and after amplification of whole repeat units) or as the result of a continuous process in which there is evidence for participation of gene conversion.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101191
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  • 4
    Electronic Resource
    Electronic Resource
    The Balbiani ring 6 induction in Chironomus
    Amsterdam : Elsevier
    Biology of the Cell 71 (1991), S. 11-16 
    Details
    ISSN: 0248-4900
    Keywords: BR genes ; Chironomus ; polytene chromosomes ; regulation of BRs ; sp-I secretory proteins ; sugar effect on BRs
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0248-4900(91)90046-P
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  • 5
    Electronic Resource
    Electronic Resource
    The c-terminal DNA-binding domain ofChironomus BR gene products shows preferential affinity for (dA,dT)-rich sequences (1996)
    Springer
    Molecular genetics and genomics 251 (1996), S. 422-427 
    Details
    ISSN: 1617-4623
    Keywords: Chironomus ; Secretory proteins ; DNA-binding ; A.T-rich DNA tracts ; DNA bending
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Balbiani ring genes (BRs), the most active loci in the polytene chromosomes of the salivary gland of the midgeChironomus (Diptera), code for secretory giant peptides (the sp-I family). Evidence previously reported indicated that the conserved C-terminal region of proteins of the sp-I family had DNA-binding properties (assayed with sp-Ia), and one such region, derived fromBR2.2, which codes for the product sp-Ib, might occur as a stable independent peptide, being transferred to the nucleus where it is detectable in the largeBRs (BR1 andBR2), among other structures, by immunostaining. Here, we show that the C-terminal portion of one of theBR gene products, expressed as a glutathione-S-transferase fusion protein shows preferential affinity for A.T-rich sequences and binds with varying affinity to restriction fragments of the A.T-rich BR1 promoter. The binding was inhibited by distamycin, suggesting that the interaction involves the minor groove of the DNA. Analysis of the promoter fragments by gel electrophoresis indicated that most appeared to present a conspicuous bend, as deduced from their anomalous electrophoretic mobilities. Furthermore, the affinity of the C-terminal domain for the different promoter fragments appeared to correlate with the degree of bending. Thus, the C-terminal domain might play a role in controlling gene expression by binding to A.T-rich sequences, including those of theBR genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02172370
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