RRNA phylogenetic comparisons

If a phylogenetic comparison is made of the 16S-Iike rRNAs from an archae-bacterium Halobacterium volcanii), a eubacterium E. coli), and a eukaryote (the yeast Saccharomyces cerevisiae), a striking similarity in secondary structure emerges (Figure 12.40). Remarkably, these secondary structures are similar despite the fact that the nucleotide sequences of these rRNAs themselves exhibit a low degree of similarity. Apparently, evolution is acting at the level of rRNA secondary structure, not rRNA nucleotide sequence. Similar conserved folding patterns are seen for the 23S-Iike and 5S-Iike rRNAs that reside in the... 

FIGURE 12.40 Phylogenetic comparison of secondary structures of 16S-Uke rRNAs from (a) a eubacterium (E. coli), (b) an archaebacterium (H. volcanii), (c) a eukaryote S. cerevisiae, a yeast). 

Figure 2. Universal phylogenetic tree determined from rRNA sequence comparisons. A matrix of evolutionary distances (99) was calculated from an alignment (260) of representative 16S RRNA sequences from each of the three urkingdoms. The length of the lines is proportional to the phylogenetic difference. (Reproduced with permission from ret 16. Copyright 19. American Society for Microbiology.)...

Fig. 1. (a) Schematic representation of the three types of anoxygenic ([1] and [2]) and oxygenic ([3]) photosynthesis found in plants and bacteria, (b) Phylogenetic tree based on 16S-rRNA sequence comparisons featuring only photo synthetic phyla. 

Fig. 1. Phylogenetic tree of the archaea indicating the phylogenetic relationship between various methanogenic genera, Archaeoglobus and Pyrococcus. The branching orders are based upon rRNA sequence comparisons according to Woese et al.[5,20] and Burggraf et al. [23]. The line lengths do not correspond to the phylogenetic distances.

The three domains of living organisms have been established by the analysis of the small-subunit rRNAs. Their comparison made it possible to divide the organisms into the three well-known kingdoms (Follmann and Brownson 2009 and Woese references cited therein). Besides rRNAs, tRNAs are among the most ancient molecules, and phylogenetic trees can be constructed from them that are not inconsistent with those constructed from rRNAs and from proteins. Keep in mind that these trees are not necessarily organismal trees. Thus, a last universal common ancestor, LUCA, was introduced (Follmann and Brownson 2009 and Woese references cited therein). The notion of LUCA is based on assumptions it is not a discrete entity. But extensive analyses have been carried out that seem to support the LUCA model. 

On the basis of the 16S/18S rRNA sequence comparisons, the hyperthermophilic bacteria (optimal growth temperature higher than 80°C) are located nearer to origins of life in the phylogenetic tree (Stetter, 1994). Therefore, many researchers think that life might have originated at temperatures as high as 100°C, before the surface of the Earth had cooled to around 30° K)°C. 

Based on their observations, they concluded that the ribosome is ribozyme and directs the catalytic properties of its all-RNA active site. The secondary structures of both 5S and 23S rRNA from H. marismortui are remarkably close to those deduced for them by phylogenetic comparison. 

S rRNA. This 120-nucleotide molecule organizes one domain of the 505 ribosomal subimit. Extensive phylogenetic comparisons of 55 RNA sequences led to the secondary structure shovm in Eig. 

Fig 4.4 Unrooted phylogenetic tree based on 16S rRNA gene comparison showing the position of rainwater (bold) and air isolates and the type strains most closely related (italic). Bootstrap probability values less than 50% were omitted from the figure. The scale bar indicates substitutions per nucleotide position. The GenBank accession numbers of type strains are in parentheses. Reproduced with permission from Marchant et al. (2008). 

Rothschild LJ, Ragan MA, Coleman AW, Heywood P, Gerbi SA (1986) Are rRNA sequence comparisons the Rosetta stone of phylogenetics. Cell 47 640... 

The unique phylogenetic position of the archaebacteria was initially proposed on the basis of sequence comparisons of one molecule, namely the 16S/18S rRNA[72], This proposal has been supported by the comparison of other rRNA and protein sequences, but the evolutionary distance of the domains relative to each other seems to vary depending on the macromolecule chosen (see ref. [73] and references therein). 

The principal characteristics of the rRNAs and of their corresponding genes, as well as the advantages to study rRNA sequences, are summarized below. Then are surveyed the most important results obtained from comparisons of rRNA sequences for the building of the so-called universal phylogenetic tree, but also for the determination of the relationships between less distantly related species. 

S rRNA has been widely used as a phylogenetic marker and the method is now well developed. There are large (and growing) public databases available which allow comparison of newly obtained sequences to already existing ones. 

Figure 1.22. Unrooted phylogenetic tree showing the positions of the test and reference strains. The tree is based on the comparison of 16S rRNA sequences, as a result of which Arachnia propionica was reclassified as Propionibacterium propionicus. The arrow indicates the estimated rooting point when Bacillus subtilis was used as a remotely related reference. Reproduced from Charfreitag et al. (1988), with permission.

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