Mutations Outside Coding Sequence

Intergenic

Mutations in introns do not affect mRNA sequence

Typical spacer Reguat°ry Exon Intron Exon Intron Exon - - 1 region gene region

Mutations here do not affect gene mRNA Exon Exon Exon unchanged

Protein A B C D E unchanged

Sequence analysis indicates that fungi are closer to being immobile animals than non-photosynthetic plants.

Sequencing of rRNA reveals that chloroplasts and mitochondria are related to the bacteria.

Although histones evolve very slowly, only eukaryotic cells possess them; they are missing from bacteria. The solution is to use ribosomal RNA. In practice, the DNA of the genes that encode the RNA of the small ribosomal subunit (16S or 18S rRNA) is sequenced and the rRNA sequence is then deduced. All living organisms have to make proteins and they all have ribosomes. Furthermore, since protein synthesis is so vital, ribosomal components are highly constrained and evolve slowly. The only group excluded is the viruses, which have no ribosomes. (Whether viruses are truly alive is debatable and their evolutionary origins are still controversial; see Ch. 17.)

Use of relationships based on ribosomal RNA has allowed the creation of large-scale evolutionary trees encompassing all the major groups of organisms. Higher organisms consist of three main groups—plants, animals and fungi (Fig. 20.17). Analysis of rRNA indicates that the ancestral fungus was never photosynthetic but split off from the plant ancestor before the capture of the chloroplast. Despite traditionally being studied by botanists, fungi are actually more closely related to animals than plants. A variety of single celled organisms sprout off the eukaryotic tree near the bottom and do not fall into any of the three major kingdoms.

As discussed in Chapter 19, most eukaryotic cells contain mitochondria and, in addition, plant cells contain chloroplasts. These organelles are derived from symbiotic bacteria and contain their own ribosomes. The rRNA sequences of mitochondria and chloroplasts reveal their relationship to the bacteria. Relationships among eukaryotes, like that shown in Fig. 20.17, are therefore made by using the rRNA of the ribosomes found in the cytoplasm of eukaryotic cells. These ribosomes have their ribosomal RNA coded for by genes in the cell nucleus.

FIGURE 20.17 Eukaryote Kingdoms Based on Ribosomal RNA Sequences

Comparing the ribosomal RNA sequences has allowed scientists to deduce how closely the major divisions of organisms are related. Protozoans such as amoebas were the earliest groups to branch from the ancestral eukaryotic lineage. A division between photosynthetic and non-photosynthetic organisms occurred next. The two branches evolved separately, the photosynthetic branch formed algae and higher plants, whereas the non-photosynthetic branch developed into ciliates, fungi and animals.

Life consists of three domains—the eubacteria, the archaebacteria and the eukaryotes.

When an rRNA-based tree is made that includes both prokaryotes and eukary-otes it turns out that life on Earth consists of three lineages (Fig. 20.18). These three domains of life are the eubacteria ("true" bacteria, including the organelles), the archaea or archaebacteria ("ancient" bacteria) and the eukaryotes. There is as much difference between the two genetically distinct types of prokaryote as between prokaryotes and eukaryotes. Sequencing of organelle rRNA indicates that mitochondria and chloroplasts belong to the eubacterial lineage.

One bizarre aspect of classifying life forms by ribosomal RNA is that the organism itself is not needed. A sample of DNA containing the genes for 16S rRNA is sufficient. Although many microorganisms present in the sea or in soil have never been successfully cultured, DNA can be extracted from the soil or seawater directly. Using PCR (see Ch. 23) it is possible to amplify the DNA from a single cell and get enough of the 16S rRNA gene to obtain a sequence. Several new groups of bacteria that branched off very early from the archaebacterial lineage have been discovered by this method, despite not being successfully cultured.

The archaebacteria are somewhat closer to the eukaryotes than to the eubacteria.

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