Evolution of the secondary structures and compensatory mutations of the ribosomal RNAs of Drosophila melanogaster

This paper examines the effects of DNA sequence evolution on RNA secondary structures and compensatory mutations. Models of the secondary structures of Drosophila melanogaster 18S ribosomal RNA (rRNA) and of the complex between 2S, 5.8S, and 28S rRNAs have been drawn on the basis of comparative and energetic criteria. The overall AU richness of the D. melanogaster rRNAs allows the resolution of some ambiguities in the structures of both large rRNAs. Comparison of the sequence of expansion segment V2 in D. melanogaster 18S rRNA with the same region in three other Drosophila species and the tsetse fly (Glossina morsitans morsitans) allows us to distinguish between two models for the secondary structure of this region. The secondary structures of the expansion segments of D. melanogaster 28S rRNA conform to a general pattern for all eukaryotes, despite having highly divergent sequences between D. melanogaster and vertebrates. The 70 novel compensatory mutations identified in the 28S rRNA show a strong (70%) bias toward A-U base pairs, suggesting that a process of biased mutation and/or biased fixation of A and T point mutations or AT-rich slippage-generated motifs has occurred during the evolution of D. melanogaster rDNA. This process has not occurred throughout the D. melanogaster genome. The processes by which compensatory pairs of mutations are generated and spread are discussed, and a model is suggested by which a second mutation is more likely to occur in a unit with a first mutation as such a unit begins to spread through the family and concomitantly through the population. Alternatively, mechanisms of proofreading in stem-loop structures at the DNA level, or between RNA and DNA, might be involved. The apparent tolerance of noncompensatory mutations in some stems which are otherwise strongly supported by comparative criteria within D. melanogaster 28S rRNA must be borne in mind when compensatory mutations are used as a criterion in secondary-structure modeling. Noncompensatory mutation may extend to the production of unstable structures where a stem is stabilized by RNA- protein or additional RNA-RNA interactions in the mature ribosome. Of motifs suggested to be involved in rRNA processing, one (CGAAAG) is strongly overrepresented in the 28S rRNA sequence. The data are discussed both in the context of the forces involved with the evolution of multigene families and in the context of molecular coevolution in the rDNA family in particular.      

Small-subunit ribosomal RNA sequence from Naegleria gruberi supports the polyphyletic origin of amoebas

We have sequenced the small-subunit ribosomal RNA gene of the amoebo- flagellate protozoan Naegleria gruberi. Comparison of this sequence with the rRNA sequences of other eukaryotes resulted in a phylogenetic tree that supports the suggested polyphyletic origin of amoebas and suggests a flagellate ancestry for Naegleria.      

Forest vegetation in relation to surface water chemistry in the North Branch of the Moose River,Adirondack Park,N.Y.

The Regional Integrated Lake-Watershed Acidification Study (RILWAS) was conducted to identify and to quantify the environmental factors controlling surface water chemistry in forested watersheds of the Adirondack region of New York. The RILWAS vegetation research was designed to: (1) compare the quantitative patterns of forest cover and tree community structure in the study catchments of the Moose River drainage system; and (2) identify important vegetation differences among study watersheds that might help to explain inter-watershed differences in water chemistry and aquatic responses to acidic deposition. Field transect data indicated that the overall drainage system includes 50% mixed forest cover, 38% hardwood forest, 10% coniferous forest, and 2% wetland cover. Major tree species include yellow birch, red spruce, American beech, sugar maple, eastern hemlock, and red maple. Analysis of forest structure indicated that mean weighted basal area estimates ranged two-fold from 24–48 m²ha^–1 among watersheds. Likewise, mean weighted estimates for aboveground biomass and aboveground annual productivity ranged among watersheds from 160 to 320 MT ha^–1 and from 8 to 18 MT ha^–1 yr^–1, respectively. Results showed that differences in surface water chemistry were independent of vegetation differences among watersheds.     

Association of allozyme heterozygosity and sternopleural chaetae number inDrosophila melanogaster

Variation at two polymorphic allozyme loci (Adh and Gpdh) has been assayed in relation to sternopleural chaetae number in flies derived from a cage population ofD. melanogaster known to be under stabilising selection with respect to chaetae number. Central phenotypes were significantly more heterozygous at these loci than more extreme phenotypes. Analysis of the base popylation and of divergent directional selection lines derived from it suggested that alleles atAdh and Gpdh have a pleiotropic effect on chaetae number or are in strong linkage disequilibrium with chaetae factors. In addition, homozygotes atAdh and Gpdh were observed to have a higher variance in chaetae number than heterozygotes. It is concluded that additive and homeostatic models of gene action might both partly explain the higher heterozygosity of central phenotypes.     

Cross-hybridizing snake satellite, Drosophila, and mouse DNA sequences may have arisen independently

Previous reports have interpreted hybridization between snake satellite DNA and DNA clones from a variety of distant taxonomic groups as evidence for evolutionary conservation, which implies common ancestry (homology) and/or convergence (analogy) to produce the cross- hybridizing sequences. We have isolated 11 clones from a genomic library of Drosophila melanogaster, using a cloned 2.5-kb snake satellite probe of known nucleotide sequence. We have also analysed published sequence data from snakes, mice, and Drosophila. These data show that (1) all of the cross-hybridization between the snake, fly, and mouse clones can be accounted for by the presence of either of two tandem repeats, [GATA]n and [GACA]n and (2) these tandem repeats are organized differently among the different species. We find no evidence that these sequences are homologous apart from the existence of the simple repeat itself, although their divergence from a common ancestral sequence cannot be ruled out. The sequences contain a variety of homogeneous clusters of tandem repeats of CATA, GA, TA, and CA, as well as GATA and GACA. We suggest that these motifs may have arisen by a self-accelerating process involving slipped-strand mispairing of DNA. Homogeneity of the clusters might simply be the result of a rate of accumulation of tandem repeats that exceeds that of other mutations.      

Skew orientation of biological samples Anacystis nidulans cyanobacteria and their fragments in a polymer matrix.

Anacystis nidulans cyanobacteria and their fragments embedded in unstretched, uniaxial and skew (two axes of stretching forming an angle of 40 degrees) stretched poly(vinyl alcohol) films have been investigated. Polarized absorption spectra for uniaxial and skew stretching samples were measured. Both unoriented and oriented samples were photographed under fluorescence microscope. In skew samples a high degree of cell orientation was reached. Skew deformation of polymer matrix compared to one axis stretching provides better band resolution in polarized absorption spectra of Anacystis nidulans samples. The shapes of absorption components measured in respect to the first and second axis of stretching are different which gives the opportunity to investigate position of various group of chlorophyll molecules in membrane.     

Genetic engineering of Bacillus subtilis for the commercial production of riboflavin

Recombinant DNA engineering was combined with mutant selection and fermentation improvement to develop a strain of Bacillus subtilis that produces commercially attractive levels of riboflavin. The B. subtilis riboflavin production strain contains multiple copies of a modified B. subtilis riboflavin biosynthetic operon (rib operon) integrated at two different sites in the B. subtilis chromosome. The modified rib operons are expressed constitutively from strong phage promoters located at the 5′ end and in an internal region of the operon. The engineered strain also contains purine analog-resistant mutations designed to deregulate the purine pathway (GTP is the precursor for riboflavin), and a riboflavin analog-resistant mutation in ribC that deregulates the riboflavin biosynthetic pathway. Received 22 June 1998/ Accepted in revised form 6 November 1998     

Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane

Molecular dynamics calculations were carried out on models of two synthetic leucine-serine ion channels: a tetrameric bundle with sequence (LSLLLSL)(3)NH(2) and a hexameric bundle with sequence (LSSLLSL)(3)NH(2). Each protein bundle is inserted in a palmitoyloleoylphosphatidylcholine bilayer membrane and solvated by simple point charge water molecules inside the pore and at both mouths. Both systems appear to be stable in the absence of an electric field during the 4 ns of molecular dynamics simulation. The water motion in the narrow pore of the four-helix bundle is highly restricted and may provide suitable conditions for proton transfer via a water wire mechanism. In the wider hexameric pore, the water diffuses much more slowly than in bulk but is still mobile. This, along with the dimensions of the pore, supports the observation that this peptide is selective for monovalent cations. Reasonable agreement of predicted conductances with experimentally determined values lends support to the validity of the simulations.