Evolution of Life on Earth

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CHAPTER 2 Evolution of Life on Earth

No one is certain how life began, but the common ancestor of all living things populated the earth over 3 billion years ago, not long (geologically speaking) after the planet formed 4.5 billion years ago (Fig. 2-1). Biochemical features shared by all existing cells suggest that this primitive microscopic cell had about 600 genes encoded in DNA, ribosomes to synthesize proteins, and a plasma membrane with pumps, carriers, and channels. Over time, mutations in the DNA created progeny that diverged genetically into numerous distinctive species, numbering about 1.7 million known to science. The total number of species living on the earth today is unknown but is estimated to be between 4 million and 100 million. On the basis of evolutionary histories preserved in their genomes, living organisms are divided into three primary domains: Bacteria, Archaea, and Eucarya.

This chapter explains our current understanding of the origin of the first self-replicating cell followed by divergence of its progeny into the two diverse groups of prokaryotes, Bacteria and Archaea. It goes on to consider theories for the origin of Eucarya and their diversification over the past 2 billion years.

Evolution is the great unifying principle in biology. Research on evolution is both exciting and challenging because this ultimate detective story involves piecing together fragmentary evidence spread over 3.5 billion years. Data include fossils of ancient organisms preserved in stone, ancient DNA (going back about 45,000 years), and especially DNA of living organisms.

Prebiotic Chemistry Leading to an RNA World

But where did the common ancestor come from? A wide range of evidence supports the idea that life began with self-replicating RNA polymers sheltered inside lipid vesicles even before the invention of protein synthesis (Fig. 2-2). This hypothetical early stage of evolution is called the RNA World. This postulate is attractive because it solves the chicken-and-egg problem of how to build a system of self-replicating molecules without having to invent either DNA or proteins on their own. Clearly, RNA has an advantage, because it provides a way to store information in a type of molecule that can also have catalytic activity. Proteins excel in catalysis but do not store self-replicating genetic information. Today, proteins have largely superseded RNAs as cellular catalysts. DNA excels for storing genetic information, since the absence of the 2′ hydroxyl makes it less reactive and therefore more stable than RNA. Readers who are not familiar with the structure of nucleic acids should consult Chapter 3 at this point.

Experts agree that the early steps toward life involved the “prebiotic” synthesis of organic molecules that became the building blocks of macromolecules. To use RNA as an example, minerals can catalyze formation of simple sugars from formaldehyde, a chemical that is believed to have been abundant on the young earth. Such reactions could have supplied ribose for ancient RNAs. Similarly, HCN and cyanoacetylene can form nucleic acid bases, although the conditions are fairly exotic and the yields are low. On the other hand, scientists still lack plausible mechanisms to conjugate ribose with a base to make a nucleoside or add phosphate to make a nucleotide without the aid of a preexisting biochemical catalyst. Nucleotides do not spontaneously polymerize into polynucleotides in water but can do so on the surface of a clay called montmorillonite. While attached to clay, single strands of RNA can act as a template for synthesis of a complementary strand to make a double-stranded RNA.

Given a supply of nucleotides, these reactions could have created a heterogeneous pool of small RNAs, the biochemical materials required to set in motion the process of natural selection at the molecular level. The idea is that random sequences of RNA are selected for replication on the basis of useful attributes. This process of molecular evolution can now be reproduced in the laboratory by using multiple rounds of error-prone replication of RNA to produce variants from a pool of random initial sequences. Given a laboratory assay for a particular function, it is possible to use this process of directed evolution to select RNAs that are capable of catalyzing biochemical reactions (called ribozymes), including RNA-dependent synthesis of a complementary RNA strand. Although unlikely, this is presumed to have occurred in nature, creating a reliable mechanism to replicate RNAs. Subsequent errors in replication produced variant RNAs, some having desirable features such as catalytic activities that were required for a self-replicating system. Over millions of years, a ribozyme eventually evolved with the ability to catalyze the formation of peptide bonds and to synthesize proteins. This most complicated of all known ribozymes is, of course, the ribosome (see Fig. 17-6) that catalyzes the synthesis of proteins. Proteins eventually supplanted ribozymes as catalysts for most biochemical reactions. Owing to greater chemical stability, DNA proved to be superior to RNA for storing the genetic blueprint over time.

Each of these events is improbable, and their combined probability is exceedingly remote, but given a vast number of chemical “experiments” over hundreds of millions of years, this all happened. Encapsulation of these prebiotic reactions may have enhanced their probability. In addition to catalyzing RNA synthesis, clay minerals can also promote formation of lipid vesicles, which can corral reactants to avoid dilution and loss of valuable constituents. This process might have started with fragile bilayers of fatty acids that were later supplanted by more robust phosphoglyceride bilayers (see Fig. 7-5). In laboratory experiments, RNAs inside lipid vesicles can create osmotic pressure that favors expansion of the bilayer at the expense of vesicles lacking RNAs.

No one knows where these prebiotic events took place. Some steps in prebiotic evolution might have occurred in hot springs and thermal vents deep in the ocean where conditions are favorable for some prebiotic reactions. Clay minerals are postulated to have had a role in forming both RNA and lipid vesicles. Carbon-containing meteorites contain useful molecules, including amino acids. Freezing of water can concentrate HCN in liquid droplets favorable for reactions leading to nucleic acid bases. Conditions for prebiotic synthesis were probably favorable beginning about 4 billion years ago, but the geologic record has not preserved convincing microscopic fossils or traces of biosynthesis older than 3.5 billion years.

Another mystery is how l-amino acids and d-sugars (see Chapter 3) were selected over their stereoisomers for biomacromolecules. This was a pivotal event, since racemic mixtures are not favorable for biosynthesis. For example, mixtures of nucleotides composed of l- and d-ribose cannot base-pair well enough for template-guided replication of nucleic acids. In the laboratory, particular amino acid stereoisomers (that could have come from meteorites) can bias the synthesis of D-sugars.

Divergent Evolution from the Last Universal Common Ancestor of Life

Shared biochemical features suggest that all current cells are derived from a last universal common ances-tor about 3.5 billion years ago (Fig. 2-1). This primitive ancestor could, literally, have been a single cell or colony of cells, but it might have been a larger community of cells sharing a common pool of genes through interchange of their nucleic acids. The situation is obscure because no primitive organisms remain. All contemporary organisms have diverged equally far in time from their common ancestor.

Although the features of the common ancestor are lost in time, this organism is inferred to have had about 600 genes encoded in DNA. It surely had messenger RNAs, transfer RNAs, and ribosomes to synthesize proteins and a plasma membrane with all three families of pumps as well as carriers and diverse channels, since these are now universal cellular constituents. The transition from primitive, self-replicating, RNA-only particles to this complicated little cell is, in many ways, even more remarkable than the invention of the RNA World. Regrettably, few traces of these events were left behind. Bacteria and Archaea that branched nearest the base of the tree of life live at high temperatures and use hydrogen as their energy source, so the common ancestor might have shared these features.

During evolution genomes have diversified by three processes (Fig. 2-3):

Gene divergence: Every gene is subject to random mutations that are inherited by succeeding generations. Some mutations change single base pairs. Other mutations add or delete larger blocks of DNA such as sequences coding a protein domain, an independently folded part of a protein (see Fig. 3-15). These events inevitably produce genetic diversity through divergence of sequences or creation of novel combinations of domains. Many mutations are neutral, but others may confer a reproductive advantage that favors persistence via natural selection. Other mutations are disadvantageous, resulting in disappearance of the lineage.

When conditions do not require the product of a gene, the gene can be lost. For example, the simple pathogenic bacteria Mycoplasma genitalium has but 470 genes, since it can rely on its animal host for most nutrients rather than making them de novo. Similarly, the slimmed-down genome of budding yeast, with only 6144 genes, lost nearly 400 genes found in organisms that evolved before fungi. Plants and fungi both lost about 200 genes required to assemble a eukaryotic cilium or flagellum—genes that characterized eukaryotes since their earliest days. Vertebrates also lost many genes that had been maintained for more than 2 billion years in earlier forms of life. For instance, humans lack the enzymes to synthesize certain essential amino acids, which must be supplied in our diets.

Evolution of Prokaryotes

Since the beginning of life, microorganisms dominated the earth in terms of numbers, variety of species, and range of habitats (Fig. 2-4). Bacteria and Archaea remain the most abundant organisms in the seas and on land. They share many features, including basic metabolic enzymes and flagella powered by rotary motors embedded in the plasma membrane. Both divisions of prokaryotes are diverse with respect to size, shape, nutrient sources, and environmental tolerances, so these features cannot be used for classification, which relies instead on analysis of their genomes. For example, sequences of the genes for ribosomal RNAs cleanly separate Bacteria and Archaea (Fig. 2-4). Bacteria are also distinguished by plasma membranes of phosphoglycerides (see Fig. 7-5

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