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 Today, proteins have largely superseded RNAs as cellular catalysts.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.

Figure 2-2 hypothesis for prebiotic evolution to last common ancestor. Simple chemical reactions are postulated to have given rise to ever more complicated RNA molecules to store genetic information and catalyze chemical reactions, including self-replication, in a prebiotic “RNA world.” Eventually, genetic information was stored in more stable DNA molecules, and proteins replaced RNAs as the primary catalysts in primitive cells bounded by a lipid membrane.

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):

Figure 2-3 mechanisms of gene diversification. A, Gene divergence from a common origin by random mutations in sister lineages creates orthologous genes. B, Gene duplication followed by divergence within and between sister lineages yields both orthologs (separated by speciation) and paralogs (separated by gene duplication). C, Lateral transfer can move entire genes from one species to another.

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) with F-type adenosine triphosphatases (ATPases) that use proton gradients to synthesize adenosine triphosphate (ATP). Archaea have plasma membranes composed of isoprenyl ether lipids and V-type ATPases that can either pump protons or synthesize ATP (see Fig. 8-5).

Figure 2-4 comparison of trees of life. A, Universal tree based on comparisons of ribosomal RNA sequences. The rRNA tree has its root deep in the bacterial lineage 3 billion to 4 billion years ago. All current organisms, arrayed at the ends of branches, fall into three domains: Bacteria, Archaea, and Eucarya (eukaryotes). This analysis assumes that the organisms in the three domains diverged from a common ancestor. The lengths of the segments and branches are based solely on differences in RNA sequences. Because the rate of random changes in rRNA genes has not been constant, the lengths of the lines that lead to contemporary organisms are not equal. Fossil records provide estimated times of a few key events. Complete sequences of some genomes (orange; see http://www.tigr.org) verify most aspects of this tree but also show that genes have moved laterally between Bacteria and Archaea and within each of these domains. Multiple bacterial genes moved to Eucarya twice: First, an α-proteobacterium fused with a primitive eukaryote, giving rise to mitochondria that subsequently transferred many of their genes to the eukaryotic nucleus; and second, a cyanobacterium fused with the precursor of algae and plants to give rise to chloroplasts. Organisms formerly classified as algae, as well as organisms formerly classified elsewhere, actually belong to four large branches near the top of the tree: alveolates (including dinoflagellates, ciliates, and sporozoans), stramenopiles (including diatoms and brown algae), rhodophytes (red algae), and plants (including the green algae). B, Composite tree based on analysis of full genome sequences and other data. This hypothesis assumes that eukaryotes formed by fusion of an α-proteobacterium with an Archaean. Chloroplasts arose from the fusion of a cyanobacterium with the eukaryotic precursor of algae and plants.

(A, Original drawing, adapted from a branching pattern from Sogin M, Marine Biological Laboratory, Woods Hole, Massachusetts. Reference: Pace N: A molecular view of microbial diversity and the biosphere. Science 276:734–740, 1997. B, Original drawing, based on multiple sources.)

Abetted by rapid proliferation and large populations, prokaryotes have used mutation and natural selection to explore many biochemical solutions to life on the earth. Some Bacteria and Archaea (and some eukaryotes too) thrive under inhospitable conditions such as anoxia and temperatures greater than 100°C as found in deep-sea hydrothermal vents. Other Bacteria and Archaea can use energy sources such as hydrogen, sulfate, or methane that are useless to eukaryotes. Fewer than 1% of Bacteria and Archaea have been grown successfully in the laboratory, so many varieties escaped detection by traditional means. New species are now identified by sequencing random DNA samples from ocean or soil or by amplifying and sequencing characteristic genes from minute samples. Only a very small proportion of bacterial species and no Archaea cause human disease.

Chlorophyll-based photosynthesis originated in Bacteria around 3 billion years ago. Surely, this was one of the most remarkable events during the evolution of life on the earth, because photosynthetic reaction centers (see Fig. 19-8) require not only genes for several transmembrane proteins but also genes for multiple enzymes to synthesize chlorophyll and other complex organic molecules associated with the proteins. Chapter 19 describes the machinery and mechanisms of photosynthesis.

Even more remarkably, photosynthesis was invented and perfected not once but twice in different bacteria. A progenitor of green sulfur bacteria and heliobacteria developed photosystem I, while a progenitor of purple bacteria and green filamentous bacteria developed photosystem II. About 2.5 billion years ago, a momentous lateral transfer event brought the genes for the two photosystems together in cyanobacteria, arguably the most important organisms in the history of the earth. Cyanobacteria (formerly misnamed blue-green algae) use an enzyme containing manganese to split water into oxygen, electrons, and protons. Sunlight energizes photosystem II and photosystem I to pump the protons out of the cell, creating a proton gradient that is used to synthesize ATP (see Chapters 8 and 19). Using sunlight as the energy source, this form of photosynthesis is the primary source of energy to synthesize the organic compounds that many other forms of life depend on for energy. In addition, beginning about 2.4 billion years ago, cyanobacteria produced most of the oxygen in the earth’s atmosphere as a by-product of photosynthesis, bioengineering the planet and radically changing the chemical environment for all other organisms as well.

Origin of Eukaryotes

Divergence from the common ancestor explains the evolution of prokaryotes but not the origin of eukaryotes. Little is known about the earliest Eucarya–neither the time of their first appearance nor much about their lifestyle–other than the fact that their genomes appear to be nearly as old (over 2 billion years) as those of Bacteria and Archaea. One problem is that early eukaryotes left no fossil record until about 1.5 billion years ago, leaving a gap of hundreds of millions of years of evolution without a physical trace except for genes that they donated to their progeny.

Therefore, researchers must analyze genome se-quences to test hypotheses about the origins of eukaryotes. The mathematical methods required to analyze the genomic data are still being perfected, and the events are so ancient that their reconstruction is challenging. The bacterial ancestor donated genes for many metabolic processes carried out in the cytoplasm. The archaeal ancestor provided many distinctive genes for informational processes such as transcription of DNA into RNA and translation of RNA into protein. This explains why eukaryotes and Archaea are neighbors on molecular phylogenies based on rRNA sequences (Fig. 2-4).

Such rRNA trees imply that eukaryotes literally branched from the lineage leading to Archaea after Archaea and Bacteria diverged from each other. Such diagrams are based on the reasonable assumption of divergence from a shared ancestor. Note, however, the long line without branches diverging from the presumed ancestor of both Archaea and eukaryotes. This poorly charted territory is responsible for the uncertainty about the origins of eukaryotes.

One attractive hypothesis is that cells from the two domains of prokaryotes joined in a symbiotic relationship to form the first eukaryote (Fig. 2-5). The identities of the Bacterium and Archaean that merged to form this hybrid cell are not known, since these were cells that lived 2 billion years ago. Such a fusion with massive lateral transfer of genes into the new organism provides a simple explanation for how both types of prokaryotes contributed to eukaryotic genomes well after their forebears diverged from the common ancestor. If two prokaryotes literally fused, then their genomes would have been in the same cytoplasm. Later, the hybrid genome was surrounded by membranes to become the nucleus, and another proteobacterium was engulfed to form the precursor of the mitochondrion.

Figure 2-5 Two possible scenarios for the origin of eukaryotes.

The more conventional view is that primitive eukaryotes first diverged from a precursor to contemporary Archaea and subsequently acquired bacterial genes by lateral transfer. One verified case of lateral transfer was the acquisition of mitochondria in the form of a symbiotic proteobacterium (see later).

Either scenario would have produced an early eukaryote endowed with a greater variety of genes than either progenitor. These single cells probably looked like prokaryotes for many millions of years before developing distinguishing features, but all traces of the original eukaryote have disappeared except for the genes that they donated to their progeny. All contemporary eukaryotes have diverged from the original eukaryote for over 2 billion years and have changed in ways that obscure the past. Although microscopic, single-celled eukaryotes called protists have been numerous and heterogeneous throughout evolution, no existing protist appears to be a good model for the ancestral eukaryote.

Origin and Evolution of Mitochondria

Overwhelming molecular evidence has established that eukaryotes acquired mitochondria when an α-proteobacterium became an endosymbiont. Modern-day α-proteobacteria include pathogenic Rickettsias. When the two formerly independent cells established a stable, endosymbiotic relationship, the Bacterium contributed molecular machinery for ATP synthesis by oxidative phosphorylation (see Fig. 19-5). The host cell might have supplied organic substrates to fuel ATP synthesis. Together, they had a reliable energy supply for processes such as biosynthesis, regulation of the internal ionic environment, and cellular motility. Given that some primitive eukaryotes lack full-fledged mitochondria, the singular event that created mitochondria was believed to have occurred well after eukaryotes branched from prokaryotes.

An alternative idea is that the recipient of the α-proteobacterium was an archaean cell rather than a eukaryote (Fig. 2-5). If so, this union could have created not only the mitochondrion but also the first eukaryote! This parsimonious hypothesis is consistent with some but not all of the available data, so it is currently impossible to rule out other scenarios.

The mitochondrial progenitor brought along its own genome and biosynthetic machinery, but over many years of evolution, most bacterial genes either moved to the host cell nucleus or were lost. Like their bacterial ancestors, mitochondria are enclosed by two membranes, with the inner membrane equipped for synthesis of ATP. Mitochondria maintain a few genes for mitochondrial components and the capacity to synthesize proteins. Nuclear genes encode most mitochondrial proteins, which are synthesized in the cytoplasm and imported into the organelle (see Fig. 18-2). The transfer of bacterial genes to the nucleus sealed the dependence of the organelle on its eukaryotic host.

Even though acquisition of mitochondria might have been the earliest event in eukaryotic evolution, some eukaryotes lack fully functional mitochondria. These lineages apparently lost most mitochondrial genes and functions through “reductive evolution” in certain anaerobic environments that did not favor natural selection for respiration. The most extreme example is the anaerobic protozoan Giardia (the cause of “hiker’s diarrhea”), which has only a remnant of a mitochondrion (used to synthesize iron-sulfur clusters for cytoplasmic ATP synthesis) and only one mitochondrial gene in the nucleus. The protist Entamoeba histolytica (another cause of diarrhea) is a less extreme example. It lacks mitochondria but has a remnant mitosome consisting of two concentric membranes with some rudimentary mitochondrial functions.

The First Billion Years of Eukaryotic Evolution

What is unique about eukaryotes? For years, it was believed that a membrane-bounded nucleus and a cytoskeleton set eukaryotes apart from prokaryotes. However, some Bacteria and Archaea have genes for homologs of the cytoskeletal proteins, actin, tubulin, and intermediate filaments. Although nuclei are rare in prokaryotes, a family of Bacteria called planctomycetes have rudimentary nuclei that also include all of the ribosomes. Thus, the three kingdoms of life have more in common than was appreciated in the past, as is fitting from our new appreciation for their common origins.

Molecular phylogenies (Fig. 2-4) indicate that modern eukaryotic lineages began to diverge during the period between 2 billion and 1 billion years ago. Since modern organisms from the earliest branches have nuclei, membrane-bounded organelles, and complex structures, including cilia for locomotion, much of what it takes to be a eukaryote evolved very early. These features require hundreds of genes that are absent from prokaryotes, but no fossils or other direct evidence are available about these early events. Organisms on early branches lack a few basic functions, such as the full machinery required for actin-based locomotion and cytokinesis, so the required genes likely appeared after their divergence.

Compartmentalization of the cytoplasm into membrane-bounded organelles is one feature of eukaryotes that is generally lacking in prokaryotes. Mitochondria might have created the first compartment. Endoplasmic reticulum, Golgi apparatus, lysosomes, and endocytic compartments came later by different mechanisms. Chloroplasts resulted from a late endosymbiotic event that occurred in algal cells (see later). Compartmentalization allowed ancestral eukaryotes to increase in size, to capture energy more efficiently, and to regulate gene expression in more complex ways.

Heterotrophic prokaryotes that obtain nutrients from a variety of sources appear to have carried out the first evolutionary experiment with compartmentalization (Fig. 2-6A). However, these prokaryotes are compartmentalized only in the sense that they separate digestion outside the cell from biosynthesis inside the cell. They export digestive enzymes (either free or attached to the cell surface) to hydrolyze complex organic macromolecules (see Fig. 18-10). They must then import the products of digestion to provide building blocks for new macromolecules. Evolution of the proteins required for targeting and translocation of proteins across membranes was a prokaryotic innovation that set the stage for compartmentalization in eukaryotes.

Figure 2-6 speculation regarding the evolution of intracellular compartments from prokaryotes to primitive eukaryotes. A–D, Possible stages in the evolution of intracellular compartments.

More sophisticated compartmentalization might have begun when a primitive prokaryote developed the capacity to segregate protein complexes with like functions in the plane of the plasma membrane. This created functionally distinct subdomains. Present-day Bacteria segregate their plasma membranes into domains specialized for energy production or protein translocation. Invagination of such domains might have created the endoplasmic reticulum (ER), Golgi apparatus, and lysosomes, as speculated in the following paragraphs (Fig. 2-6):

This divide-and-specialize strategy might have been employed a number of times to refine the internal membrane system. Eventually, the export and digestive pathways separated from each other and from the lipid synthetic and protein translocation machinery.

As each specialized compartment became physically separated from other compartments, new mechanisms were required to allow traffic between these compartments. The solution was transport vesicles to export products to the cell surface or vacuole and to import raw materials. Transport vesicles also segregated digestive enzymes from the surrounding cytoplasm. Once multiple destinations existed, targeting instructions had to be provided to distinguish the routes and destinations.

The outcome of these events (Fig. 2-7) was a vacuolar system consisting of the ER, the center for protein translocation and lipid synthesis; the Golgi complex and secretory pathway, for posttranslational modification and distribution of biosynthetic products to different destinations; and the endosome/lysosome system, for uptake and digestion.

Figure 2-7 membrane-bounded compartments of eukaryotes. A, Pathways for endocytosis and degradation of ingested materials. B, Pathways for biosynthesis and distribution of proteins, lipids, and polysaccharides. Membrane and content move through these pathways by controlled budding of vesicles from donor compartments and fusion with specific acceptor compartments. Transport of membranes and content through these two pathways is balanced to establish and maintain the sizes of the compartments.

Production of oxygen by photosynthetic cyanobacteria raised the concentration of atmospheric oxygen about 2.2 billion years ago. This provided sufficient molecular oxygen for eukaryotic cells to synthesize cholesterol (see Fig. 20-14). Incorporation of cholesterol might have strengthened the plasma membrane without compromising fluidity and enabled early eukaryotic cells to increase in size and shed their cell walls. Having shed their cells walls, they could engulf entire prey organisms rather than relying on extracellular digestion. The increase in oxygen also precipitated most of the dissolved iron in the world’s oceans, creating ore deposits that are being mined today to extract iron.

The origins of peroxisomes are obscure. No nucleic acids or prokaryotic remnants have been detected in peroxisomes, so it seems unlikely that peroxisomes began as prokaryotic symbionts. Peroxisomes arose as centers for oxidative degradation, particularly of products of lysosomal digestion that could not be reutilized for biosynthesis (e.g., d-amino acids, uric acid, xanthine). One possibility is that they evolved as a specialization of endoplasmic reticulum.

Origins and Evolution of Chloroplasts

The acquisition of plastids, including chloroplasts, began when a cyanobacterial symbiont brought photosynthesis into a primitive algal cell that already had a mitochondrion (Fig. 2-8). The cyanobacterium provided both photosystem I and photosystem II, allowing the sunlight to provide energy to split water and to drive conversion of CO₂ into organic compounds with O₂ as a by-product (see Fig. 19-8). Symbiosis turned into complete interdependence when most of the genes that are required to assemble plastids moved to the nucleus of host cells that continued to rely on the plastid to capture energy from sunlight. This still-mysterious transfer of genes to the nucleus gave the host cell control over the replication of the former symbiont.

Figure 2-8 acquisition of chloroplasts. This is a time line from left to right. The primary event was the ingestion of a cyanobacterium by the eukaryotic cell that gave rise to red algae, glaucophytes, and green algae. Green algae gave rise through divergence to land plants. Diatoms, dinoflagellates, and euglenoids acquired chloroplasts by secondary (S1 through S7) or tertiary (T1) symbiotic events when their precursors ingested an algae with chloroplasts.

(Based on Falkowski PG, Katz ME, Knoll AH, et al: Evolution of modern eukaryotic phytoplankton. Science 305:354–360, 2004.)

Many animals and protozoa associate with photosynthetic bacteria or algae, but the conversion of a bacterial symbiont into a plastid is believed to have been a singular event. The original photosynthetic eukaryote then diverged into three lineages: green algae, red algae, and a minor group of photosynthetic unicellular organisms called glaucophytes (Fig. 2-8). Green algae, such as the experimentally useful model organism Chlamydomonas (see Fig. 38-20), are still plentiful. Green algae also gave rise through divergence to about 300,000 species of land plants.

Events following the initial acquisition of chloroplasts were more complicated, since in at least seven instances, new eukaryotes acquired photosynthesis by taking in an entire green or red alga, followed by massive loss of algal genes. These secondary symbiotic events left behind chloroplasts along with the nuclear genes required for chloroplasts. For example, precursors of Euglena took up whole green algae, as did one family of dinoflagellates and chloroarachinophytes. Red algae participated in four secondary and one tertiary symbiotic events, giving rise to diatoms and some of the dinoflagellates. Today, photosynthesis by these marine microbes converts CO₂ into much of the oxygen and organic matter on the earth.

These secondary symbiotic events make phylogenetic relationships of nuclear genes and chloroplast genes discordant in these organisms. For example, ribosomal RNA gene sequences show that Euglena diverged well before algae and later acquired a chloroplast related to those of green algae. The phylogenetic relationships of dinoflagellates are particularly complex, given that a common host cell acquired chloroplasts from three separate sources.

Evolution of Multicellular Eukaryotes

Since the origin of life on the earth, most living organisms have consisted of a single cell. Single-celled prokaryotes, protists, algae, and fungi still dominate the planet. Colonial bacteria initiated evolutionary experiments in living together over 2 billion years ago. About 1 billion years ago, the major branches of eukaryotes—fungi; cellular slime molds; red, brown, and green algae; and animals—independently evolved strategies to form multicellular organisms (Fig. 2-9).

Figure 2-9 time line for the divergence of animals, plants, and fungi. This tree has a radial time scale originating about 1100 million years (my) ago with the last common ancestor of plants, animals, and fungi. Contempo-rary organisms and time are at the circumference. Lengths of branches are arbitrary. The order of branching is established by comparisons of gene sequences. The times of the earliest branching events are only estimates, since calibration of the molecular clocks is uncertain and the early fossil records are sparse.

(Original drawing, based on timing for animals, adapted from Kuman S, Hedges SB: A molecular time scale for vertebrate evolution. Nature 392:917–920, 1998; based on timing for plants, adapted from Green Plant Phylogeny Research Coordination Group at http://ucjeps.herb.berkeley.edu/bryolab/greenplantpage.html; based on timing for fungi, adapted from Tree of Life Web Project at http://tolweb.org/tree.)

Algae and plants separated from the cells that gave rise to fungi and animals about 1100 million years ago. This estimate is probably correct, in spite of a general lack of fossils of these lineages older than 550 million years. Early fungi may simply be difficult to distinguish from their progenitors. Molecular phylogenetics have not yet resolved unambiguously the branching of about 5000 species of red, brown, and green algae. More recent branches, such as the evolution of plants from green algae, are better established.

Fossils of early metazoans (multicellular animals) are difficult to find because they are so tiny. The same may be true for early plants. A few well-preserved, 600-million-year-old fossils show that animals already had complex, bilaterally symmetrical bodies at this early date. These tiny (180μm long) animals had three tissue layers, a mouth, a gut, a coelomic cavity, and surface specializations that are speculated to be sensory structures. Formation of such tissues required membrane proteins for adhesion to the extracellular matrix and to other cells (see Chapter 30). Genes for adhesion proteins—including proteins related to cadherins, integrins, and Ig-CAMs—are found in species that branched before metazoans, so their origins are ancient. Other 570-million-year-old fossils are similar to contemporary animal embryos. These spectacular microscopic fossils support the hypothesis that early multicellular animals were small creatures similar to contemporary invertebrate larvae or embryos. Animals appear to have existed much earlier but have not yet been found in the fossil record.

The early metazoans had little in common with contemporary animals, except possibly sponges, and many were lost to extinction. As evolutionary experimentation progressed, sponges (Porifera) were the first branch of metazoans that survives today. The cells of these colonial organisms have much in common with ciliated protozoa called Chonoflagellates. Next to this branch, about 700 million years ago, were the Cnidarians: jellyfish and corals. These animals have specialized epithelial, nerve, and muscle cells in two layers.

About 540 million to 520 million years ago, conditions allowed the emergence of macroscopic multicellular animals. At the time of this “Cambrian explosion,” metazoans became abundant in numbers and varieties in the fossil record. The appearance of these animals in the fossil record over a short period of time is a puzzle, since evolution of such complex body plans must actually have taken a long time. The likely explanation is that the major branches of the animal tree diverged before macroscopic animals developed, as indicated by analysis of genome sequences. Owing to their small size and lack of hard body parts, these progenitors left behind few recognizable fossils.

About 600 million years ago, all other animals branched off as three subdivisions of organisms with bilateral symmetry (at some time in their lives), three tissue layers (ectoderm, mesoderm, and endoderm), and complex organs. The three subdivisions are arthropods and nematodes; mollusks, annelid worms, brachiopods, and platyhelmiths; and echinoderms and chordata (including us).

Looking Back in Time

Viewing contemporary eukaryotic cells, one should be awed by the knowledge that they are mosaics created by historical events that occurred over a vast range of time. Roughly 3.5 billion years ago, the common ancestors of living things already stored genetic information in DNA; transcribed genes into RNA; translated mRNA into protein on ribosomes; carried out basic intermediary metabolism; and were protected by plasma membranes with carriers, pumps, and channels. More than 2.5 billion years ago, bacteria evolved the genes required for photosynthesis and eventually donated this capacity to eukaryotes via endosymbiosis about 1 billion years ago. An α-proteobacterium took up residence in an early eukaryote, giving rise to mitochondria about 2 billion years ago. Although prokaryotes have genes for homologs of all three cytoskeletal proteins, eukaryotes developed the capacity for cellular motility about 1.5 billion years ago when they shed their cell walls and evolved genes for molecular motors and many proteins that regulate the cytoskeleton. Multicellular eukaryotes with specialized cells and tissues arose only in the past 1.2 billion years after acquiring plasma membrane receptors used for cellular interactions.

It is also instructive to consider how more complex functions, such as the operation of the human nervous system, have their roots deep in time, beginning with the advent of molecules such as receptors and voltage-sensitive ion channels that originally served their unicellular inventors. At each step along the way, evolution has exploited the available materials for new functions to benefit the multitude of living organisms.

Internet

Deep Green Tree of Life Web Project. Available at http://tolweb.org/tree/phylogeny.html.

ACKNOWLEDGMENTS

Some of this chapter comes from material written by Ann L. Hubbard, J. David Castle, and Sandra Schmid for the first edition of Cell Biology. Thanks also go to Steve Stearns, Mike Donoghue, Mitch Sogin, Jim Lake, Daniel Pollard, Katherine Pollard, and Leslie Orgel.