Читать книгу Molecular Mechanisms of Photosynthesis - Robert E. Blankenship - Страница 23

There are many ways to organize and classify life. No one method is inherently superior to any other, as all such systematic organizations are ultimately only for our benefit. Classification methods are usually structured to accomplish a desired goal, such as rapid identification of organisms in the field or the laboratory. One of the most informative ways to classify organisms is based on evolutionary relationships. This evolutionary, or phylogenetic, approach has led to the recognition that there are three fundamental domains of living organisms: bacteria, archaea (formerly called archaebacteria), and eukarya. This division of the tree of life into the three domains is based on a classification of organisms according to the small subunit rRNA method introduced by Carl Woese (Fig. 2.1). This method relies on comparisons of the sequences of RNA molecules that are part of the ribosome, the protein‐synthesizing particle. For bacteria and archaea, the RNA molecule that is used is known as 16S rRNA, while for eukaryotes it is a related molecule known as 18S rRNA. The S stands for Svedberg units, which derive from early methods of molecular weight determination using ultracentrifuges. The basis of this molecular evolution method is the fact that the positional order, or sequence, of building blocks of a biological macromolecule retains information about the evolutionary history of the organism. Two organisms that are closely related will have macromolecules (DNA, RNA, or proteins) whose sequences are highly similar, while distantly related organisms will have sequences that have diverged in the long time interval since their common ancestor. The selection of the rRNA molecule as the molecular chronometer is based on the fact that this molecule is universally present in all organisms, has the same function in all organisms, and has an excellent dynamic range. Parts of the molecule change slowly and are therefore useful for establishing distant evolutionary relationships, while other parts change more rapidly and are therefore more useful for fine distinctions among more closely related organisms.

The rRNA molecules are thought to be a proxy for the evolutionary relationships of the entire organisms that are being compared. This view is something of an oversimplification, because the method actually establishes only the evolutionary relationships of the rRNA molecule, which is part of the protein synthesis machinery of the cell. However, the rRNA molecules appear to be only very rarely transferred from one cell type to another, a process known as horizontal gene transfer. All these reasons make the rRNA molecules a good proxy for the evolutionary history of the organism as a whole. A tree of organismal evolutionary relationships is often called a species tree.

Figure 2.1 Small subunit rRNA phylogenetic tree of Life, with division into the three domains of bacteria, archaea, and eukarya. The highlighted taxa contain photosynthetic organisms. The color coding represents the type of reaction center complex found in the organism, with purple indicating Type II reaction centers and green indicating Type I reaction centers. The red arrow indicates the endosymbiotic origin of chloroplasts from cyanobacteria.

Source: Blankenship (2010) (p. 435)/The American Society of Plant Biologists.

It is clear from analysis of complete genome sequences for many organisms that there has been significant horizontal transfer of genetic information among various bacteria and even between bacteria and eukaryotes (Soucy et al., 2015). Therefore, the image of a single, branching evolutionary tree that applies to all organisms is increasingly being replaced by a more complex netlike arrangement, in which some parts of an organism bear different evolutionary relationships to other organisms (Doolittle, 1999). However, the process of horizontal gene transfer has apparently not been so extensive as to blur the essential distinctions among the different groups of organisms, as the groupings according to more traditional classification methods are reasonably consistent with those predicted by the RNA analysis, at least in broad outline.

The evolutionary history of any gene or gene family reflects the development of that gene, regardless of what organism has been its host during the course of evolution. An evolutionary tree of a particular gene is therefore called a gene tree and may be very different from the species tree of organisms. The origin and early evolution of life with special emphasis on photosynthesis are discussed in more detail in Chapter 12.