Resurrection of an ancestral 5S rRNA

<p>Abstract</p> <p>Background</p> <p>In addition to providing phylogenetic relationships, tree making procedures such as parsimony and maximum likelihood can make specific predictions of actual historical sequences. Resurrection of such sequences can be used to understand early events in evolution. In the case of RNA, the nature of parsimony is such that when applied to multiple RNA sequences it typically predicts ancestral sequences that satisfy the base pairing constraints associated with secondary structure. The case for such sequences being actual ancestors is greatly improved, if they can be shown to be biologically functional.</p> <p>Results</p> <p>A unique common ancestral sequence of 28 <it>Vibrio </it>5S ribosomal RNA sequences predicted by parsimony was resurrected and found to be functional in the context of the <it>E. coli </it>cellular environment. The functionality of various point variants and intermediates that were constructed as part of the resurrection were examined in detail. When separately introduced the changes at single stranded positions and individual double variants at base-paired positions were also viable. An additional double variant was examined at a different base-paired position and it was also valid.</p> <p>Conclusions</p> <p>The results show that at least in the case of the 5S rRNAs considered here, ancestors predicted by parsimony are likely to be realistic when the prediction is not overly influenced by single outliers. It is especially noteworthy that the phenotype of the predicted ancestors could be anticipated as a cumulative consequence of the phenotypes of the individual variants that comprised them. Thus, point mutation data is potentially useful in evaluating the reasonableness of ancestral sequences predicted by parsimony or other methods. The results also suggest that in the absence of significant tertiary structure constraints double variants that preserve pairing in stem regions will typically be accepted. Overall, the results suggest that it will be feasible to resurrect additional meaningful 5S rRNA ancestors as well as ancestral sequences of many different types of RNA.</p

Differentiation, growth and morphogenesis: Acetabularia as a model system

The aim of this paper is to review the present knowledge of the main aspects of differentiation of Acetabularia, a unicellular, eukaryotic organism, and to underline the multiple control pathways modulated by circadian rhythmicity. Growth and morphogenesis are sequentially programmed. Timing of cap differentiation is highly dependent on external conditions. The importance of the sequence of processes is shown by experimental disregulation. The alga is a highly polarized cell, both in morphology and in the relative concentrations of a number of the molecules it contains. Apical cap differentiation is regulated at the post-transcriptional level and could also depend in part on polyamines and on proteolytic activity. Acetabularia displays a number of circadian rhythms (CR). These rhythms form an elaborate biological time structure (also called temporal morphology, or morphology in time as opposed to morphology in space): the distribution in the 24 h cycle of the peaks and troughs of the oscillating functions. The oscillations display fixed relations both with the other functions and with external conditions (such as the transition from dark to light). Interestingly, the CR modulate Acetabularia's development, which is influenced by photoperiod; we present preliminary experiments suggesting that disruption of temporal morphology is deleterious to morphogenesis. Induction of growth and of morphogenesis are totally dependent on blue light. However, blue light receptors in plants are probably multiple, but we present arguments suggesting that flavin-cytochrome b and the associated SHAM-sensitive molecule are present in Acetabularia plasma membrane and are involved in blue light perception. Agents interfering with different steps of signal perception and transduction show that at least some of these steps are temporally regulated. According to recent experiments from our laboratory, the existence of a redox signalling mechanism appears to be highly probable. The phytohormones (or plant regulators), auxin (indole acetic acid), abscisic acid and ethylene, exert cell-regulatory functions and are involved in Acetabularia differentiation. They also modulate at least some circadian rhythms. Finally, circadian rhythms intervene in differentiation and are proposed to have an integrative function.SCOPUS: re.jFLWINinfo:eu-repo/semantics/publishe