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22.1B: The Origins of Archaea and Bacteria - Biology

22.1B: The Origins of Archaea and Bacteria - Biology


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Archaea are believed to have evolved from gram-positive bacteria and can occupy more extreme environments.

Learning Objectives

  • Distinguish bacteria from archaea in terms of their origins

Key Points

  • The first prokaryotes were adapted to the extreme conditions of early earth.
  • It has been proposed that archaea evolved from gram-positive bacteria as a response to antibiotic selection pressures.
  • Microbial mats and stromatolites represent some of the earliest prokaryotic formations that have been found.

Key Terms

  • stromatolite: a laminated, columnar, rock-like structure built over geologic time by microorganisms such as cyanobacteria
  • gram-positive: that is stained violet by Gram’s method due to the presence of a peptidoglycan cell wall
  • sacculus: a small sac
  • indel: either an insertion or deletion mutation in the genetic code

Prokaryotes, the First Inhabitants of Earth

When and where did life begin? What were the conditions on earth when life began? Prokaryotes were the first forms of life on earth, existing for billions of years before plants and animals appeared. The earth and its moon are thought to be about 4.54 billion years old. This estimate is based on evidence from radiometric dating of meteorite material together with other substrate material from earth and the moon. Early earth had a very different atmosphere (contained less molecular oxygen) than it does today and was subjected to strong radiation; thus, the first organisms would have flourished where they were more protected, such as in ocean depths or beneath the surface of the earth. Also at this time, strong volcanic activity was common on Earth. It is probable that these first organisms, the first prokaryotes, were adapted to very high temperatures. Early earth was prone to geological upheaval and volcanic eruption, and was subject to bombardment by mutagenic radiation from the sun. The first organisms were prokaryotes that could withstand these harsh conditions.

Although probable prokaryotic cell fossils date to almost 3.5 billion years ago, most prokaryotes do not have distinctive morphologies; fossil shapes cannot be used to identify them as Archaea. Instead, chemical fossils of unique lipids are more informative because such compounds do not occur in other organisms. Some publications suggest that archaean or eukaryotic lipid remains are present in shales dating from 2.7 billion years ago. Such lipids have also been detected in Precambrian formations. The oldest such traces come from the Isua district of west Greenland, which include earth’s oldest sediments, formed 3.8 billion years ago. The archaeal lineage may be the most ancient that exists on earth.

Within prokaryotes, archaeal cell structure is most similar to that of gram-positive bacteria, largely because both have a single lipid bilayer and usually contain a thick sacculus of varying chemical composition. In phylogenetic trees based upon different gene / protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of Gram-positive bacteria. Archaea and gram-positive bacteria also share conserved indels in a number of important proteins, such as Hsp70 and glutamine synthetase.

It has been proposed that the archaea evolved from gram-positive bacteria in response to antibiotic selection pressure. This is suggested by the observation that archaea are resistant to a wide variety of antibiotics that are primarily produced by gram-positive bacteria and that these antibiotics primarily act on the genes that distinguish archaea from bacteria. The evolution of Archaea in response to antibiotic selection, or any other competitive selective pressure, could also explain their adaptation to extreme environments (such as high temperature or acidity) as the result of a search for unoccupied niches to escape from antibiotic-producing organisms.

Microbial Mats

Microbial mats or large biofilms may represent the earliest forms of life on earth; there is fossil evidence of their presence starting about 3.5 billion years ago. A microbial mat is a multi-layered sheet of prokaryotes that includes mostly bacteria, but also archaea. Microbial mats are a few centimeters thick, typically growing where different types of materials interface, mostly on moist surfaces. The various types of prokaryotes that comprise the mats use different metabolic pathways, which is the reason for their various colors. Prokaryotes in a microbial mat are held together by a glue-like sticky substance that they secrete called extracellular matrix.

The first microbial mats likely obtained their energy from chemicals found near hydrothermal vents. A hydrothermal vent is a breakage or fissure in the earth’s surface that releases geothermally-heated water. With the evolution of photosynthesis about 3 billion years ago, some prokaryotes in microbial mats came to use a more widely-available energy source, sunlight, whereas others were still dependent on chemicals from hydrothermal vents for energy and food.

Stromatolites

Fossilized microbial mats represent the earliest record of life on earth. A stromatolite is a sedimentary structure formed when minerals are precipitated out of water by prokaryotes in a microbial mat. Stromatolites form layered rocks made of carbonate or silicate. Although most stromatolites are artifacts from the past, there are places on earth where stromatolites are still forming. For example, growing stromatolites have been found in the Anza-Borrego Desert State Park in San Diego County, California.


This Strange Microbe May Mark One of Life’s Great Leaps

An organism living in ocean muck offers clues to the origins of the complex cells of all animals and plants.

A bizarre tentacled microbe discovered on the floor of the Pacific Ocean may help explain the origins of complex life on this planet and solve one of the deepest mysteries in biology, scientists reported on Wednesday.

Two billion years ago, simple cells gave rise to far more complex cells. Biologists have struggled for decades to learn how it happened.

Scientists have long known that there must have been predecessors along the evolutionary road. But to judge from the fossil record, complex cells simply appeared out of nowhere.

The new species, called Prometheoarchaeum, turns out to be just such a transitional form, helping to explain the origins of all animals, plants, fungi — and, of course, humans. The research was reported in the journal Nature.

“It’s actually quite cool — it’s going to have a big impact on science,” said Christa Schleper, a microbiologist at the University of Vienna who was not involved in the new study.

Our cells are stuffed with containers. They store DNA in a nucleus, for example, and generate fuel in compartments called mitochondria. They destroy old proteins inside tiny housekeeping machines called lysosomes.

Our cells also build themselves a skeleton of filaments, constructed out of Lego-like building blocks. By extending some filaments and breaking others apart, the cells can change their shape and even move over surfaces.

Species that share these complex cells are known as eukaryotes, and they all descend from a common ancestor that lived an estimated two billion years ago.

Before then, the world was home only to bacteria and a group of small, simple organisms called archaea. Bacteria and archaea have no nuclei, lysosomes, mitochondria or skeletons.

Evolutionary biologists have long puzzled over how eukaryotes could have evolved from such simple precursors.

In the late 1900s, researchers discovered that mitochondria were free-living bacteria at some point in the past. Somehow they were drawn inside another cell, providing new fuel for their host.

In 2015, Thijs Ettema of Uppsala University in Sweden and his colleagues discovered fragments of DNA in sediments retrieved from the Arctic Ocean. The fragments contained genes from a species of archaea that seemed to be closely related to eukaryotes.

Dr. Ettema and his colleagues named them Asgard archaea. (Asgard is the home of the Norse gods.) DNA from these mystery microbes turned up in a river in North Carolina, hot springs in New Zealand and other places around the world.

Asgard archaea rely on a number of genes that previously had been found only in eukaryotes. It was possible that these microbes were using these genes for the same purposes — or for something else.

“Until you have an organism, you cannot really be sure,” said Dr. Schleper.

Masaru K. Nobu, a microbiologist at the National Institute of Advanced Industrial Science and Technology in Tsukuba, Japan, and his colleagues managed to grow these organisms in a lab. The effort took more than a decade.

The microbes, which are adapted to life in the cold seafloor, have a slow-motion existence. Prometheoarchaeum can take as long as 25 days to divide. By contrast, E. coli divides once every 20 minutes.

The project began in 2006, when researchers hauled up sediment from the floor of the Pacific Ocean. Initially, they hoped to isolate microbes that eat methane, which might be used to clean up sewage.

In the lab, the researchers mimicked the conditions in the seafloor by putting the sediment in a chamber without any oxygen. They pumped in methane and extracted deadly waste gases that might kill the resident microbes.

The mud contained many kinds of microbes. But by 2015, the researchers had isolated an intriguing new species of archaea. And when Dr. Ettema and colleagues announced the discovery of Asgard archaea DNA, the Japanese researchers were shocked. Their new, living microbe belonged to that group.

The researchers then undertook more painstaking research to understand the new species and link it to the evolution of eukaryotes.

The researchers named the microbe Prometheoarchaeum syntrophicum, in honor of Prometheus, the Greek god who gave humans fire — after fashioning them from clay.

“The twelve years of microbiology it took to get to the point where you can see it down a microscope is just amazing,” said James McInerney, an evolutionary biologist at the University of Nottingham who was not involved in the research.

Under the microscope, Prometheoarchaeum proved to be a strange beast. The microbe starts out as a tiny sphere, but over the course of months, it sprouts long, branching tentacles and releases a flotilla of membrane-covered bubbles.

It proved even stranger when the researchers examined the cell’s interior. Dr. Schleper and other researchers had expected that Asgard archaea used their eukaryote-like proteins to build some eukaryote-like structures inside their cells. But that’s not what the Japanese team found.

“On the inside, there’s no structure, just DNA and proteins,” said Dr. Nobu.

This finding suggests that the proteins that eukaryotes used to build complex cells started out doing other things, and only later were assigned new jobs.

Dr. Nobu and his colleagues are now trying to figure out what those original jobs were. It’s possible, he said, that Prometheoarchaeum creates its tentacles with genes later used by eukaryotes to build cellular skeletons.

Dr. Schleper wanted to see more evidence for this idea. “There are very nice arms on other archaea,” she observed. But those other species aren’t using proteins so similar to ours.

Before the discovery of Prometheoarchaeum, some researchers suspected that the ancestors of eukaryotes lived as predators, swallowing up smaller microbes. They might have engulfed the first mitochondria this way.

But Prometheoarchaeum doesn’t fit that description. Dr. Nobu’s team often found the microbe stuck to the sides of bacteria or other archaea.

Instead of hunting prey, Prometheoarchaeum seems to make its living by slurping up fragments of proteins floating by. Its partners feed on its waste. They, in turn, provide Prometheoarchaeum with vitamins and other essential compounds.

Dr. Nobu speculated that a species of Asgard archaea on the seafloor dragged bacteria into a web of tentacles, drawing them into even more intimate association. Ultimately, it swallowed the bacteria, which evolved into the mitochondria fueling every complex cell.

Dr. McInerney was skeptical that Prometheoarchaeum could provide a clear picture of how our ancestors took in mitochondria two billion years ago. “This is an organism alive today in 2020,” he said.

As Dr. Nobu’s team continues to study Prometheoarchaeum, they’re also hunting for its relatives in their seafloor mud. Those microbes may turn out to be even closer to our own ancestry — and may offer even more unexpected clues.


22.2 Structure of Prokaryotes

In this section, you will explore the following questions:

  • What are similarities in the structures of the prokaryotes, Archaea and Bacteria?
  • What are examples of structural differences between Archaea and Bacteria?

Connection for AP ® Courses

Domains Archaea and Bacteria contain single-celled organisms lacking a nucleus and other membrane-bound organelles. The two groups have substantial biochemical and structural differences. Most have a cell wall external to the plasma cell membrane, the composition of which can vary among groups, and many have additional structures such as flagella and pili. Prokaryotes also have ribosomes, where protein synthesis occurs. For the purpose of AP ® , you do not have to memorize the various groups of bacteria. You should, however, be able to distinguish between prokaryotes and eukaryotes and know the domains.

Teacher Support

  • Provide students with multiple opportunities to summarize the similarities and differences between prokaryotic and eukaryotic cells and between cells in the three domains (Eukarya, Archaea, Bacteria). You may wish to ask students to sketch typical cells of each class or domain, create tables comparing and contrasting the cellular and genomic organization in each, or complete other short activities. When discussing similarities and differences, be sure to offer or ask for qualifying details where it makes sense to do so. (For example, cell walls are found in prokaryotes and some eukaryotes the material of which they are made is quite different.)
  • When reviewing prokaryotic reproduction, take time to connect new information to students’ previous knowledge. For example, remind students of the importance of genetic diversity as discussed in chapters on evolutionary theory. Emphasize that although new mutations are a major source of variation (as they learned in previous chapters), additional diversity arises in prokaryotic populations from genetic recombination. Stress that while eukaryotes carry out the sexual processes of meiosis and fertilization that combine DNA from two individuals, prokaryotes uses other processes (transformation, transduction, and conjugation) to bring together DNA from different individuals. You may wish to ask students to consider the advantages of several modes of genetic recombination for a population.

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 2 and Big Idea 3 of the AP ® Biology Curriculum Framework. The AP ® Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® exam questions. A learning objective merges required content with one or more of the seven science practices.

Big Idea 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis.
Enduring Understanding 2.B Growth, reproduction and dynamic homeostasis require that cell create and maintain internal environments that are different form their external environment.
Essential Knowledge 2.B.3 Archaea and Bacteria generally lack internal membranes and organelles.
Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively.
Learning Objective 2.14 The student is able to use representations and models to describe differences in prokaryotic and eukaryotic cells.
Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes.
Enduring Understanding 3.C The processing of genetic information is imperfect and is a source of genetic variation.
Essential Knowledge 3.C.2 Prokaryotes contain circular chromosomes and plasmid DNA.
Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices.
Learning Objective 3.27 The student is able to compare and contrast processes by which genetic variation is produced and maintained in organisms from multiple domains.
Essential Knowledge 3.C.2 Prokaryotes contain circular chromosomes and plasmid DNA.
Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas.
Learning Objective 3.28 The student is able to construct an explanation of the multiple processes that increase variation within a population.

The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
[APLO 2.5][APLO 2.13][APLO 2.14][APLO 4.9]

There are many differences between prokaryotic and eukaryotic cells. However, all cells have four common structures: the plasma membrane, which functions as a barrier for the cell and separates the cell from its environment the cytoplasm, a jelly-like substance inside the cell nucleic acids, the genetic material of the cell and ribosomes, where protein synthesis takes place. Prokaryotes come in various shapes, but many fall into three categories: cocci (spherical), bacilli (rod-shaped), and spirilli (spiral-shaped) (Figure 22.9).

The Prokaryotic Cell

Recall that prokaryotes (Figure 22.10) are unicellular organisms that lack organelles or other internal membrane-bound structures. Therefore, they do not have a nucleus but instead generally have a single chromosome—a piece of circular, double-stranded DNA located in an area of the cell called the nucleoid. Most prokaryotes have a cell wall outside the plasma membrane.

Recall that prokaryotes are divided into two different domains, Bacteria and Archaea, which together with Eukarya, comprise the three domains of life (Figure 22.11).

The composition of the cell wall differs significantly between the domains Bacteria and Archaea. The composition of their cell walls also differs from the eukaryotic cell walls found in plants (cellulose) or fungi and insects (chitin). The cell wall functions as a protective layer, and it is responsible for the organism’s shape. Some bacteria have an outer capsule outside the cell wall. Other structures are present in some prokaryotic species, but not in others (Table 22.2). For example, the capsule found in some species enables the organism to attach to surfaces, protects it from dehydration and attack by phagocytic cells, and makes pathogens more resistant to our immune responses. Some species also have flagella (singular, flagellum) used for locomotion, and pili (singular, pilus) used for attachment to surfaces. Plasmids, which consist of extra-chromosomal DNA, are also present in many species of bacteria and archaea.

Characteristics of phyla of Bacteria are described in Figure 22.12 and Figure 22.13 Archaea are described in Figure 22.14.

The Plasma Membrane

The plasma membrane is a thin lipid bilayer (6 to 8 nanometers) that completely surrounds the cell and separates the inside from the outside. Its selectively permeable nature keeps ions, proteins, and other molecules within the cell and prevents them from diffusing into the extracellular environment, while other molecules may move through the membrane. Recall that the general structure of a cell membrane is a phospholipid bilayer composed of two layers of lipid molecules. In archaeal cell membranes, isoprene (phytanyl) chains linked to glycerol replace the fatty acids linked to glycerol in bacterial membranes. Some archaeal membranes are lipid monolayers instead of bilayers (Figure 22.14).

The Cell Wall

The cytoplasm of prokaryotic cells has a high concentration of dissolved solutes. Therefore, the osmotic pressure within the cell is relatively high. The cell wall is a protective layer that surrounds some cells and gives them shape and rigidity. It is located outside the cell membrane and prevents osmotic lysis (bursting due to increasing volume). The chemical composition of the cell walls varies between archaea and bacteria, and also varies between bacterial species.

Bacterial cell walls contain peptidoglycan, composed of polysaccharide chains that are cross-linked by unusual peptides containing both L- and D-amino acids including D-glutamic acid and D-alanine. Proteins normally have only L-amino acids as a consequence, many of our antibiotics work by mimicking D-amino acids and therefore have specific effects on bacterial cell wall development. There are more than 100 different forms of peptidoglycan. S-layer (surface layer) proteins are also present on the outside of cell walls of both archaea and bacteria.

Bacteria are divided into two major groups: Gram positive and Gram negative, based on their reaction to Gram staining. Note that all Gram-positive bacteria belong to one phylum bacteria in the other phyla (Proteobacteria, Chlamydias, Spirochetes, Cyanobacteria, and others) are Gram-negative. The Gram staining method is named after its inventor, Danish scientist Hans Christian Gram (1853–1938). The different bacterial responses to the staining procedure are ultimately due to cell wall structure. Gram-positive organisms typically lack the outer membrane found in Gram-negative organisms (Figure 22.15). Up to 90 percent of the cell wall in Gram-positive bacteria is composed of peptidoglycan, and most of the rest is composed of acidic substances called teichoic acids. Teichoic acids may be covalently linked to lipids in the plasma membrane to form lipoteichoic acids. Lipoteichoic acids anchor the cell wall to the cell membrane. Gram-negative bacteria have a relatively thin cell wall composed of a few layers of peptidoglycan (only 10 percent of the total cell wall), surrounded by an outer envelope containing lipopolysaccharides (LPS) and lipoproteins. This outer envelope is sometimes referred to as a second lipid bilayer. The chemistry of this outer envelope is very different, however, from that of the typical lipid bilayer that forms plasma membranes.

Visual Connection

  1. Gram-positive bacteria have a cell wall anchored to the cell membrane by lipoteichoic acid.
  2. Porins allow entry of substances into both Gram-positive and Gram-negative bacteria.
  3. The cell wall of Gram-negative bacteria is thick, and the cell wall of Gram-positive bacteria is thin.
  4. Gram-negative bacteria have a cell wall made of peptidoglycan, whereas Gram-positive bacteria have a cell wall made of lipoteichoic acid.

Archaean cell walls do not have peptidoglycan. There are four different types of Archaean cell walls. One type is composed of pseudopeptidoglycan, which is similar to peptidoglycan in morphology but contains different sugars in the polysaccharide chain. The other three types of cell walls are composed of polysaccharides, glycoproteins, or pure protein.

Structural Characteristic Bacteria Archaea
Cell type Prokaryotic Prokaryotic
Cell morphology Variable Variable
Cell wall Contains peptidoglycan Does not contain peptidoglycan
Cell membrane type Lipid bilayer Lipid bilayer or lipid monolayer
Plasma membrane lipids Fatty acids Phytanyl groups

Reproduction

Reproduction in prokaryotes is asexual and usually takes place by binary fission. Recall that the DNA of a prokaryote exists as a single, circular chromosome. Prokaryotes do not undergo mitosis. Rather the chromosome is replicated and the two resulting copies separate from one another, due to the growth of the cell. The prokaryote, now enlarged, is pinched inward at its equator and the two resulting cells, which are clones, separate. Binary fission does not provide an opportunity for genetic recombination or genetic diversity, but prokaryotes can share genes by three other mechanisms.

In transformation, the prokaryote takes in DNA found in its environment that is shed by other prokaryotes. If a nonpathogenic bacterium takes up DNA for a toxin gene from a pathogen and incorporates the new DNA into its own chromosome, it too may become pathogenic. In transduction, bacteriophages, the viruses that infect bacteria, sometimes also move short pieces of chromosomal DNA from one bacterium to another. Transduction results in a recombinant organism. Archaea are not affected by bacteriophages but instead have their own viruses that translocate genetic material from one individual to another. In conjugation, DNA is transferred from one prokaryote to another by means of a pilus, which brings the organisms into contact with one another. The DNA transferred can be in the form of a plasmid or as a hybrid, containing both plasmid and chromosomal DNA. These three processes of DNA exchange are shown in Figure 22.17.

Reproduction can be very rapid: a few minutes for some species. This short generation time coupled with mechanisms of genetic recombination and high rates of mutation result in the rapid evolution of prokaryotes, allowing them to respond to environmental changes (such as the introduction of an antibiotic) very quickly.

Evolution Connection

The Evolution of Prokaryotes

How do scientists answer questions about the evolution of prokaryotes? Unlike with animals, artifacts in the fossil record of prokaryotes offer very little information. Fossils of ancient prokaryotes look like tiny bubbles in rock. Some scientists turn to genetics and to the principle of the molecular clock, which holds that the more recently two species have diverged, the more similar their genes (and thus proteins) will be. Conversely, species that diverged long ago will have more genes that are dissimilar.

Scientists at the NASA Astrobiology Institute and at the European Molecular Biology Laboratory collaborated to analyze the molecular evolution of 32 specific proteins common to 72 species of prokaryotes. 2 The model they derived from their data indicates that three important groups of bacteria—Actinobacteria, Deinococcus, and Cyanobacteria (which the authors call Terrabacteria)—were the first to colonize land. (Recall that Deinococcus is a genus of prokaryote—a bacterium—that is highly resistant to ionizing radiation.) Cyanobacteria are photosynthesizers, while Actinobacteria are a group of very common bacteria that include species important in decomposition of organic wastes.

The timelines of divergence suggest that bacteria (members of the domain Bacteria) diverged from common ancestral species between 2.5 and 3.2 billion years ago, whereas archaea diverged earlier: between 3.1 and 4.1 billion years ago. Eukarya later diverged off the Archaean line. Stromatolites are some of the oldest fossilized organisms on Earth at around 3.5 million years ago. There is evidence that these prokaryotes were also some of the first photosynthesizes on Earth. In fact, bacterial prokaryotes were likely responsible for the first accumulation of oxygen in our atmosphere through photosynthesis. The group Terrabacteria possessed many adaptations for living on land, such as resistance to drying. Some of these adaptations were also related to photosynthesis, such as compounds that protect cells from excess light. These early prokaryotic pathways related to photosynthesis were the foundation for photosynthesis in eukaryotic cells. This is evidenced by the similarity in structure and function between some photosynthetic prokaryotes and eukaryotic chloroplasts.


Domain Cell Theory supports the independent evolution of the Eukarya, Bacteria and Archaea and the Nuclear Compartment Commonality hypothesis

In 2015, the Royal Society of London held a meeting to discuss the various hypotheses regarding the origin of the Eukarya. Although not all participants supported a hypothesis, the proposals that did fit into two broad categories: one group favoured ‘Prokaryotes First’ hypotheses and another addressed ‘Eukaryotes First’ hypotheses. Those who proposed Prokaryotes First hypotheses advocated either a fusion event between a bacterium and an archaeon that produced the first eukaryote or the direct evolution of the Eukarya from the Archaea. The Eukaryotes First proponents posit that the eukaryotes evolved initially and then, by reductive evolution, produced the Bacteria and Archaea. No mention was made of another previously published hypothesis termed the Nuclear Compartment Commonality (NuCom) hypothesis, which proposed the evolution of the Eukarya and Bacteria from nucleated ancestors (Staley 2013 Astrobiol Outreach1, 105 (doi:10.4172/2332-2519.1000105)). Evidence from two studies indicates that the nucleated Planctomycetes–Verrucomicrobia–Chlamydia superphylum members are the most ancient Bacteria known (Brochier & Philippe 2002 Nature417, 244 (doi:10.1038/417244a) Jun et al. 2010 Proc. Natl Acad. Sci. USA107, 133–138 (doi:10.1073/pnas.0913033107)). This review summarizes the evidence for the NuCom hypothesis and discusses how simple the NuCom hypothesis is in explaining eukaryote evolution relative to the other hypotheses. The philosophical importance of simplicity and its relationship to truth in hypotheses such as NuCom and Domain Cell Theory is presented. Domain Cell Theory is also proposed herein, which contends that each of the three cellular lineages of life, the Archaea, Bacteria and Eukarya domains, evolved independently, in support of the NuCom hypothesis. All other proposed hypotheses violate Domain Cell Theory because they posit the evolution of different cellular descendants from ancestral cellular types.

1. Introduction

Carl Woese used the small subunit rRNA to construct the scientific Tree of Life [1]. This phylogenetic tree provided evidence that life consists of three domains, the Bacteria, Archaea and Eukarya. The major question this review addresses is ‘What hypothesis best explains the evolution of the three domains, and in particular, the Eukarya?’

That the origin of the Eukarya is still a hotly debated subject is attested to by the contributions to a recent meeting of the Royal Society in London in 2015 [2]. Some participants did not commit to a hypothesis, but those who did fell into two primary camps. Most advocated a ‘Prokaryotes First’ hypothesis and one paper discussed the various ‘Eukaryotes First’ hypotheses.

Those who favoured ‘Prokaryotes First’ hypotheses trace their ideas most recently to the Ring Theory of Life [3]. A basic argument of the Prokaryotes First proponents is that, because prokaryotic (before nucleus) organisms are simpler and evolution leads to greater complexity, the prokaryotes, i.e. the Bacteria and Archaea, must have been the first organisms.

Mariscal & Doolittle [4] summarized a different set of hypotheses from scientists who favoured a ‘Eukaryotes First’ hypothesis. The major claim of these advocates is that the Eukarya must have evolved first to produce the Bacteria and Archaea because it is simpler to produce a prokaryote from a eukaryote by reductive evolution than vice versa.

Unfortunately, an entirely different hypothesis termed the Nuclear Compartment Commonality (NuCom) hypothesis [5] was not discussed at the meeting although it was published prior to the meeting. NuCom posits that the Bacteria and Eukarya evolved from nucleated ancestors. The Bacteria evolved from nucleated ancestors of the Planctomycetes–Verrucomicrobia–Chlamydia (PVC) superphylum. In addition, it posits that the Eukarya have always been nucleated. A major purpose of this paper is to briefly summarize and then provide a critique of the Prokaryotes First and Eukaryotes First hypotheses. This is followed by information about NuCom, a ‘Nucleated Organisms First’ hypothesis, because it is virtually unknown to biologists.

Finally, cell theory will be discussed. Current cell theory holds that every cell comes from a cell. Domain Cell Theory, proposed below, states that when the domains of life evolved, each of the three domains evolved from separate and unique cellular lineages.

2. Terminology

The PVC Bacteria are the PVC superphylum [6], some members of which are nucleated, i.e. their DNA and DNA replication, and probably also transcription, occur in a membrane bound compartment composed of glycerol 3-phosphate with sn-1,2 stereochemistry linked to the fatty acid side chains by ester bonds (G3P PLFA). Some species such as Gemmata obscuriglobus have cellular compartments with nuclei [7]. In addition to the PVC phyla, the phyla Lentisphaerae and Poribacteria may also be members of the PVC superphylum.

Enucleation is the process whereby a nucleated organism loses its nuclear compartment through reductive evolution. For example, nucleated ancestors of the Verrucomicrobia may have evolved to produce the Proteobacteria because both contain methanotrophic bacteria, use the Calvin–Benson carbon dioxide fixation process and contain prosthecate bacteria [5,8].

Common bacteria are defined as typical Bacteria, like Escherichia coli, a proteobacterium whose DNA is not contained in a nuclear compartment.

Protokaryote (Greek proto meaning ‘first’ and karyon ‘nucleus’) refers to the pre-domain ancestral cell state of the last universal common ancestor (LUCA). NuCom proposes that the ancestor of the PVC Bacteria and the Eukarya were two emergent phylogeneticaly distinct protokaryotic lineages with a simple nuclear compartment (figure 1).

Figure 1. Illustration showing the evolution of the Bacteria and Eukarya from LUCA. The bounding cell and nuclear membranes of the Bacteria (red nucleus) and Eukarya (blue nucleus) have an essentially identical chemical composition, however the genomes contain divergent genetic material.

Protokaryotic signature proteins (PSPs) are homologous proteins currently found as remnants in certain representatives of the PVC superphylum as well as almost all representatives of the Eukarya (some have termed these ‘eukaryotic signature proteins').

Eukaryogenesis is defined as the continuous evolution of eukaryote cellular complexity and organization in this unique domain.

3. Summary and critique of hypotheses

3.1. Prokaryotes First hypotheses

A popular view held by many is that the Archaea are the ancestors of the Eukarya either by evolving directly to produce the Eukarya [9] or via an unproven and untestable fusion event between an archaeon and a bacterium. This latter view is commonly held by most microbiologists who regard the Bacteria and Archaea as prokaryotes, which implies that they were the first organisms that later gave rise to the nucleated Eukarya via a hypothetical fusion event.

Advocates of Prokaryotes First hypotheses at the 2015 Royal Society meeting fell into two groups:

Group A: Fusion event occurred between a bacterium and an archaeon that led to the evolution of the Eukarya

Fusion advocates have invoked the synthesis of the eukaryotic cell from the biological merger between a bacterium with an archaeon. The most challenging issue facing the ‘Prokaryotes First’ fusion advocates is that they need to explain how two highly divergent cell types produced a protoeukaryote. This is difficult to explain from three primary standpoints.

Firstly, and perhaps most importantly, if fusion occurred it was a ‘once-only’ or singular event. This singular event cannot be reproduced in the laboratory or subjected to rigorous scientific study. From a philosophical standpoint, a hypothesis that is not verifiable or falsifiable is unscientific [10] and therefore invalid.

Secondly, several questions remain unanswered. For example, how did the resulting eukaryote retain one cell membrane type rather than another? Several groups question, for example, the ability of an archaeon to engulf a bacterium, a necessary step in the entrainment of a mitochondrion in eukaryotic evolution [11,12] and fusion hypotheses in general [13].

Thirdly, this hypothesis is in violation of Domain Cell Theory because one cellular lineage was created by the fusion of two different cell types (see below).

Group B: The Archaea were the direct ancestors of the Eukarya

Other ‘Prokaryotes First’ advocates propose that the Archaea, alone, evolved to produce the Eukarya [9]. This currently popular view has been favoured more recently especially because of environmental genomic studies such as the recent discovery of the ‘Lokiarchaeum’ group of Archaea, in which evidence for ‘complex eukaryotic genes' has been found in environmental genome libraries [14].

Williams & Embley [9] proposed a two domain tree of the Bacteria and Archaea in which the Archaea evolved to produce the Eukarya. Their tree can be seriously questioned from other scientific information. For example, how did the Eukarya acquire their G3P PLFA membranes from an archaeon whose ether-linked membranes are completely different [15]? In addition, Gribaldo et al. [16] raise doubt about sufficient evidence for a monophyletic lineage containing the Archaea/Eukarya.

Both groups of the Prokaryotes First school of thought have retained an early view of organism evolution that believes eukaryotes must have evolved from simpler organisms. There is virtually no evidence that this is what actually happened.

Also, some microbiologists proposed that the PVC superphylum is ancestral to the Eukarya. More recently, McInerny et al. [17] rebutted this hypothesis. The view that the PVC group evolved to become the Eukarya was also doubted by Staley et al. [18], who conducted the first genomic study of a member of the Verrucomicrobia (Prosthecobacter dejongeii) and a Planctomycete (Gemmata strain Wa1-1). That study concluded it was unlikely that the PVC superphylum gave rise to the Eukarya.

Although the latter reference agreed with most of the conclusions of McInerny et al., this author believes they wrongly regarded the ‘ESPs’ (eukaryotic signature proteins), such as bacterial tubulin and serine threonine kinase (STK) genes as horizontal gene transfers (HGTs) from Eukarya [18,19]. By regarding these ancient proteins as being more recent transfers from eukaryotic organisms, they have denied the PVC bacteria of their ancient heritage as discussed below in a more recent paper supporting the NuCom hypothesis [19]. This last reference regards these ancient proteins as remnants from LUCA that were essential in the early evolution of the nucleated Bacteria and Eukarya. As such, they provide important phylogenetic evidence for the early commonality between the Bacteria and Eukarya.

Significantly, although most of these ancient proteins have been explained as more recent HGT events by some [17], the enzymes responsible for cell membrane synthesis are unlikely to be due to HGT primarily because membranes must have pre-dated the origin of cellular life [19]. Further, so far as is known, all the enzymes of the Bacteria and Eukarya that are responsible for the synthesis of G3P PLFA membranes are homologous [15], supporting the commonality of cell membranes in LUCA for the Bacteria and Eukarya, and the NuCom hypothesis. One might, though, also predict homologous membrane enzymes from Prokaryotes First hypotheses which propose the alpha-proteobacterium ancestor of the mitochondrion was engulfed by the Archaea host that evolved to produce the Eukarya. However, those hypotheses must explain how the mitochondrial G3P PLFA membrane replaced the ether-linked membrane of the host archaeon in view of arguments for Simplicity and the Cellular Compatibility (discussed later in this paper).

3.2. Eukaryotes First hypotheses

Hypotheses of the Eukaryotes First proponents were also presented at the Royal Society meeting [4], with various views of those who believe that the Bacteria and Archaea are descended from nucleated, eukaryotic organisms. However, as Woese's Tree of Life indicates, the Eukarya did not give rise to the Bacteria because they appear on a completely separate branch of the Tree of Life.

This author agrees with one very important point that the Eukaryotes First proponents espouse, namely that it is simpler to produce a prokaryote from a eukaryote (i.e. a nucleated organism) than to produce a eukaryote from one or two prokaryotes. This point of view is consistent with the NuCom hypothesis that explains the evolution of the Bacteria and Eukarya from nucleated ancestors.

4. Nuclear Compartment Commonality hypothesis

The NuCom hypothesis [5,19] states that both the Eukarya and the Bacteria evolved from nucleated ancestors during the period that DNA replication evolved. This is in agreement with the view that the Eukarya comprise an independent domain and have always been nucleated [20]. A more precise timetable regarding this is not possible at this time without additional information, but the section Eukaryogenesis below states that it may have occurred about 3.0 Ga bp.

According to NuCom, the Bacteria are also descended from nucleated organisms. Phylogenetic evidence supporting NuCom comes from two independent groups. One group provided phylogenetic information from highly conserved regions of 16S rDNA [21] that indicates the Planctomycetes are the most ancient Bacteria. Likewise, Jun et al. [22] arrived at the same conclusion using proteomic phylogenies. Ancestors of the nucleated PVC superphylum are hypothesized by NuCom to be ancestral to all other Bacteria including the enucleate Common Bacteria.

The Common Bacteria are regarded as having become enucleate by reductive evolution from PVC superphylum ancestors. The rationale for this is that by maintaining a smaller and less complex genome, they could compete more efficiently for their niches. The example given in the original NuCom hypothesis is that of the Verrucomicrobia giving rise to the Proteobacteria [5]. Both groups contain the only methanotrophic members of the Bacteria and share other features as well, such as prosthecae and the Calvin–Benson cycle. Most importantly, a 16S rRNA phylogenetic tree supports the view that the Verrucomicrobia were the ancestors of the Proteobacteria [8].

Further phylogenetic support for NuCom comes from ancient PSPs such as α- and β-homologues of tubulin that have been found in the PVC superphylum. These proteins have been called ESPs by many because they are found in phylogenetic trees with eukaryote homologues. By contrast, these proteins, which are found in a few representatives of the PVC superphylum, are regarded as PSPs of LUCA by the NuCom hypothesis because of their ancient phylogeny. They occur as remnants in certain species indicating that reductive evolution has occurred in PVC phyla as well as in the enucleate Common Bacteria but their presence in the PVC reveals their deep ancestry from LUCA.

Finally, and perhaps most importantly, the NuCom hypothesis is the simplest hypothesis to explain the origin of the Eukarya. The Simplicity analysis, which regards the simplest hypotheses and theories to be more likely true philosophically, is used in physics and in chemistry, although much less often in biology. Hypotheses and theories that are the most simple are considered not only most likely to be true, but are also aesthetically more favourable [23]. This argument applies to both the NuCom hypothesis and Domain Cell Theory because they require much less complexity to explain the evolution of the Bacteria and Eukarya.

5. Eukaryogenesis

Prokaryotes First advocates believe that the Eukarya arose later in time because fossil evidence for them is non-existent until about 1.5–2.0 Ga bp. However, NuCom regards that eukaryotes evolved during the time that DNA replication evolved in the PVC Bacteria. The NuCom hypothesis explains the later appearance of the Eukarya in the fossil record by a series of stages of a long process of complexification termed eukaryogenesis (dates below are approximate).

Stage A. Evolution of DNA replication in LUCA.

When DNA replication evolved in LUCA it gave rise to two disparate lineages, the Bacteria and the Eukarya. Therefore, both lineages date to about 3.0 Ga bp.

(1) Cells were unicellular with only a membrane enveloping them—therefore they did not leave identifiable fossil traces.

(2) Few cells were formed because they had a poor energy source—they probably were fermentative and lived off available sugars.

(3) No exceptional, unique products were produced by eukaryal metabolism—unlike methanogenic Archaea which give rise to 12 C-fractionated methane or Bacteria such as the Cyanobacteria that produced oxygen.

(4) Actin evolution began about 2.5 Ga bp. This led to the ability of Eukarya to engulf foodstuffs, the singular early means that still characterizes the unique eukaryal feeding mode, phagocytosis. Notably, we as human omnivores still use it and make a big fuss about it, too!

(1) The mitochondrion evolved from an aerobic member of the Alphaproteobacteria which, after engulfment, was entrained by symbiosis within the ancestor of all Eukarya. This enormously enhanced their ability to make ATP.

(2) These early Eukarya were still unicellular and difficult to detect because they lacked cell walls.

(3) The Cellular Compatibility argument (see below) provides a rationale for how a bacterium became the mitochondrion.

Stage D. Period of evolution of mitosis, meiosis and sexuality and larger, more complex multicellular organisms. About 2.0–l.5Ga bp until the present.

Eukaryogenesis occurred over many millions of years, but it was not until they had fully evolved that the Eukarya as we know them today could be readily detected in the fossil record.

Although the early stages (A – early stage D) could not have been easily detected in the fossil record, by about 1.5–2.0 Ga bp, the evolution of the Eukarya eventually gave rise to the more readily detectable contemporary single and multicellular organisms including certain protists, algae, plants and animals.

6. Homlogous proteins found in Planctomycetes–Verrucomicrobia–Chlamydia Bacteria and Eukarya

Several examples of ancient highly conserved proteins (PSPs) are found in the PVC superphylum as well as the Eukarya. A summary of this information is provided below that supports the common origin of these proteins in LUCA and the nucleated descendants of the PVC Bacteria and Eukarya.

6.1. Cell membrane enzyme homologues

As noted previously, the cell membranes (and hence nuclear membranes of the nucleated organisms) of the Bacteria and Eukarya are identical so far as is known. They both comprise G3P PLFA. The pathway for their synthesis is also identical so far as is known, including homologous enzymes for each of the steps [15]. This is prima facie evidence for the ancient common ancestry of these PSPs in both Bacteria and Eukarya completely in accord with NuCom.

Some have proposed these cell membrane proteins (enzymes) represent HGTs between the Bacteria and Eukarya. For example, in their review Poole & Penny [24] discuss one unlikely scenario that suggests the eukaryotic membrane may have been derived from the bacterial mitochondrial endosymbiont of the purported archaeon ancestor as discussed previously.

Interestingly, although cell and nuclear membranes represent early commonalities between the Bacteria and Eukarya, their genomes diverged from one another enormously and gave rise to the two most plentiful and diverse forms of life on Earth.

Most importantly, these cell membrane proteins are found in all Bacteria, not simply the PVC superphylum. These ancient membrane proteins from LUCA provide irrevocable testimony to a common origin of the Bacteria and the Eukarya that is consistent with NuCom.

The following ancient PSPs found in the PVC superphylum have been regarded by others as due to HGT from a eukaryote. However, there is no basis for this other than that they are found in phylogenetic trees close to those of the Eukarya. NuCom rightly reclaims them as PSPs derived from LUCA and not examples of HGT events.

6.2. Tubulin

Perhaps the most remarkable protein reported in the PVC superphylum is tubulin. The α- and β-homologues of tubulin have been found in all members of the Eukarya. Lynn Margulis, an early proponent of Prokaryotes First concepts, hypothesized that tubulins came from the spirochetes, which was consistent with her view that the spirochetes evolved tubulin that provided motility to some immotile protists. However, no spirochete genome has ever been reported to contain tubulin genes whereas some of the Verrocomicrobia do. Several species of the Prosthecobacter genus contain the highly conserved tubulin proteins bacterial tubulin A (BtubA) and bacterial tubulin B (BtubB) which are homologous to α- and β- eukaryotic tubulin, respectively [25].

FtsZ is a much smaller homologue of tubulin that is found in all Bacteria and some of the Archaea and is required for cell division. Importantly, FtsZ is also found in the tubulinate Prosthecobacter species [19], suggesting it is necessary for cell division. Aside from these bacteria, no other known species of the Bacteria or the Archaea is known to have tubulin homologues.

6.3. Ubiquitin system and serine/threonine kinases

The ubiquitin system contains enzymes that are responsible for the degradation of proteins and is found in all eukaryotes. Eukaryote-like serine/threonine kinases (STKs) and E2-ubiquitin-conjugating enzymes are also found in the PVC superphylum, including members of the Planctomycetes [26], Chlamydia and Verrucomicrobia.

6.4. Sterol synthesis

Some members of the Planctomycetes contain sterols in their cell membranes which are also found in the Eukarya as well as some Common Bacteria. Importantly, the sterol synthesis pathway in the Gemmata genus contains deeply rooted enzymes (PSPs) consistent with their origin in LUCA [19], although some have inferred they are another example of HGT between the Eukarya and Bacteria [27]. The extensive pathway network found in Pirellula staleyi provides strong support for the pathway in extant members of the PVC superphylum [19].

7. Other support for Nuclear Compartment Commonality

Studies of the phylogeny of ancient protein folding families (FF) are also consistent with NuCom [28]. These authors report that early evolution progressed in five phases as shown in Venn diagrams. The initial phase indicated there were 76 shared FF among all three domains. The final Phase V contained 484 FF shared among the three domains. At stage V, however, the total number of protein FF found in the Archaea was only 703, whereas there were 1510 in the Bacteria and 1656 in the Eukarya. Further, this paper indicates that the Archaea branched off LUCA with these fewer FF compared with the Bacteria and Eukarya, which remained together before later diverging dramatically as sister groups, is in accord with Woese's Tree of Life.

This perspective article also proposes the Domain Cell Theory of Life which supports the NuCom hypothesis because Woese's three domains of life comprise three independent cellular lineages. Fusion between two cellular types does not occur. The entrainment of an alpha-proteobacterium to become a mitochondrion and a cyanobacterium to become a chloroplast in the Eukarya do not change the fundamental cellular type of the Eukarya in which they became endosymbionts.

8. Domain Cell Theory of Life

Schleiden and Schwann proposed the cell theory of life which states that all living organisms are cellular. All cells are derived from pre-existing cells. As stated by Virchow in 1859 [29], ‘every cell from a cell’ (omnis cellula e cellula).

The Tree of Life provides a further elaboration of the meaning of cell theory. This is herein named Domain Cell Theory, which posits that the domains in Carl Woese's Tree of Life comprise three different cellular types: Archaea, Bacteria and Eukarya.

— All Bacteria have cell membranes containing glycerol 3-phosphate with sn-1,2 stereochemistry linked to the fatty acid side chains by ester bonds (G3P PLFA).

— All Bacteria have or have had peptidoglycan cell walls during their evolution.

— The PVC superphylum contains the most ancient members of the Bacteria, some of which are nucleated.

— All Eukarya have cell membranes containing glycerol 3-phosphate with sn-1,2 stereochemistry linked to the fatty acid side chains by ester bonds (G3P PLFA).

— All members of the Eukarya contain a nucleus with nuclear membranes.

— Eukaryogenesis describes the process by which Eukaryotic cells evolved engulfment of particulate materials (phagocytosis), mitosis, meiosis and sexuality.

— All Archaea have glycerol 1-phosphate (G1P) ether linkages in their cell membranes.

In particular, each of the three cellular lineages is distinct from the other two on the basis of cellular evolution, genetic composition and cell envelope types, which include cell and nuclear membrane and cell wall, if present. This is logical because cell membranes must have existed at the time LUCA gave rise to the three separate domain lineages. Domain Cell Theory states that the descendants of each of the three domains retained its identity throughout its own unique evolutionary pathway.

A primary feature or tenet of Domain Cell Theory is that it is not possible to produce a different cell type from the fusion of two other cellular types as proposed by ‘Prokaryotes First’ proponents. Another characteristic is that it is impossible for one cellular type to become a different cellular type, such as the direct evolution of the Eukarya from the Archaea [9]. Accordingly, all ‘Prokaryotes First’ hypotheses are invalid by Domain Cell Theory which is in agreement with the NuCom hypothesis.

Likewise, the various ‘Eukaryotes First’ proposals that the Archaea and Bacteria evolved from the Eukarya are also contrary to the Tree of Life, which clearly indicates a separate evolution of all three cellular lineages. In particular, the Eukaryotes First proponents propose that the Eukarya evolved by reductive evolution to produce the Bacteria and Archaea. This is also a violation of Domain Cell Theory. Thus, none of the Prokaryotes First or the Eukaryotes First hypotheses is valid.

Further support for Domain Cell Theory is that, of all the thousands of Bacteria, Archaea and Eukarya that have been studied, each of them can be placed into one of the three domains of life. If cellular types are freely able to change, then one should ask, ‘Where are the intermediate types or species among these three different domains?’ To my knowledge, none exist.

Regarding Domain Cell Theory discussed above, two mitigating factors need to be mentioned. The first is that viruses are known to play a very important role in transferring genes from one organism to another, which could lead to the introduction of genes into different lineages. An especially interesting proposal is that the three domains of life originated in an RNA world in which, during the transition to DNA, three different founder DNA viruses gave rise to the three domains of organisms [30].

In addition, HGT is also known to be a mechanism to transfer genes from one group of organisms to another. However, it is noteworthy that these events, including viral transfer, typically occur between closely related taxa. Unfortunately, HGT has been sometimes misused to support hypotheses that are otherwise unsupportable.

9. Cellular Compatibility argument

It is interesting to note that modifications of cells do occur within at least two of the domains, the Bacteria and the Eukarya. Regarding the Bacteria, according to NuCom, the original nucleated ancestors of the PVC superphylum gave rise to the enucleate Common Bacteria which lost their nuclei through reductive evolution [5]. This probably occurred to enable Common Bacteria to fit more efficiently into their specialized niches that required less energy. This process does not violate cell theory in that the cell envelope of all Bacteria still contains peptidoglycan as well as the G3P PLFA membranes. Earlier it was thought that the Planctomycetes lacked peptidoglycan, but more recently it has been found in two different members of the phylum [31,32], indicating that all bacteria contain it except for those such as bacterial L-forms that have lost it.

With respect to the Eukarya, all species have a mitochondrion or did have a mitochondrion during their evolution. Those that no longer have mitochondria lost them through reductive evolution. This is explained by Cellular Compatibility as follows. The proto-eukaryotic cells lacked mitochondria because the Alphaproteobacteria lineage that gave rise to the mitochondrion had not evolved until approximately 2 Ga bp. Because cell membranes of the Bacteria and Eukarya are highly similar, the two cellular types are compatible. The engulfed pre-mitochondrion lost its peptidoglycan layer during the entrainment process making it compatible within eukaryotic cells. A similar argument can be made for chloroplasts that are derived from Cyanobacteria that were entrained in algae following ingestion by single-celled protists enabling them to become photosynthetic. Interestingly, these entrained cells also lost their peptidoglycan. The plants that also have cell walls evolved from the algae with cyanobacterial chloroplasts.

By contrast, there is no evidence that the Archaea produced intracellular organelles of or in the Bacteria or Eukarya. Cellular incompatibility may account for this because the archaeal cell envelopes are markedly different from the Bacteria or Eukarya. Although the evolution of the Archaea is not discussed here, their evolution was independent from that of the Bacteria and Eukarya because of their unique cell envelope features and generally smaller genomes. This is in agreement with the Tree of Life and the NuCom hypothesis.

10. Discussion

Carl Woese's Tree of Life was a seminal event in biology because it was the first scientific Tree of all organisms on Earth. His Tree of Life actually revealed that the Archaea comprise a separate, third branch of life that was previously unknown. What is so surprising is that the interpretation of the Tree of Life has been so controversial.

Three main lines of thought have contributed to the confusion about what the Tree of Life means:

Life evolved from prokaryotic organisms, the Bacteria and Archaea, because they are simpler than the Eukarya and evolution leads to greater complexity

Students of microbiology are taught about prokaryotic organisms. Since ‘pro’ means ‘before’ this implies that the Bacteria and Archaea were the first organisms, i.e. prior to the Eukarya. Secondly, many regard evolution as a process that always leads to complexity, so simple organisms, i.e. prokaryotes, probably evolved to produce nucleated organisms. Proponents of ‘Prokaryotes First’ hypotheses frequently believe that the Bacteria and Archaea contain all the genetic information necessary to produce a eukaryotic organism.

All members of the Bacteria including the PVC superphylum are prokaryotic

Although members of the PVC superphylum contain nuclei, many microbiologists either do not know this or they expect these cannot be nuclei because they are not identical to those of the Eukarya despite the marked divergence of the Bacteria from the Eukarya as shown by the Tree of Life. They then further deny the PVC superphylum of their remarkable phylogenetic characteristics such as the PSP proteins which are among the most complex and significant phylogenetic markers confirming their ancient heritage in LUCA. Their explanation for their occurrence in the PVC superphylum is, without evidence, that they have been transferred by HGT from the Eukarya.

The Eukarya did not evolve until about 1.5–2.0Ga bp

Because the Eukarya did not leave a fossil record until about 1.5 Ga bp, many believe it was because they evolved more recently than the Bacteria and Archaea. This view also promotes the idea of Prokaryotes First hypotheses.

As discussed here, this author believes that all three of these views are misconceptions that have led to incorrect interpretations of the meaning of the Tree of Life. A simple examination of Woese's Tree shows there are three major, independent lines of descent, the Bacteria, Eukarya and Archaea, leading to the concept of three domains. Moreover, the late appearance of the Eukarya which is clearly indicated by the long branch of this lineage in Woese's Tree of Life is not because they evolved last, but because their complete evolution required much more time and they did not leave detectable evidence in the fossil record until much later. Present-day eukaryotes required hundreds of millions of years of evolution to attain the hallmarks of the present-day Eukarya: complex genomes with mitochondria that could carry out mitosis and meiosis, sexuality and could develop noticeable traces of their existence in the fossil record.

Of course those who believe that the Eukarya evolved first do not accept the Prokaryotes First interpretation either. However, their idea that the Eukarya evolved to produce the Bacteria and Archaea does not fit with Woese's Tree either because each of life's domains is independent from the others.

This paper also posits the Domain Cell Theory, which is an extension of Cell Theory. As clearly shown in Carl Woese's Tree, there are three independent cellular lineages of life. The product of each led to a descendant cell type of its own kind: Bacteria from Bacteria, Archaea from Archaea and Eukarya from Eukarya.

The NuCom hypothesis is the only one that complies with Domain Cell Theory. All Prokaryotes First and Eukaryotes First hypotheses violate Domain Cell Theory.


3. How old?

Microbial life can be traced back to the Archaean (greater than 2500 million years ago) based on the ratios of biogenic isotopes distinctive of different metabolisms, but also on microfossils traces and biomarkers. The most ancient reliable biomarkers for bacterial (and possibly eukaryal) life are given by the presence of hopanes and steranes in 2.7 Gyr Archaean shales (Brocks et al. 1999 Summons 1999). On the contrary, extended isoprene chains (greater than C20), which are good fossil biomarkers for archaeal lipids, are less stable and have only been found in rocks up to 1.6 Gyr old (Summons et al. 1988). However, the isotopic record of ultralight carbon indicates the presence of methane of biological origin (i.e. methanogenesis) at 2.7 Gyr ago (Ga) (Hayes 1994). In addition, evidence of sulphate reduction at 3.4 Ga (Shen et al. 2001) suggests that anaerobic consortia of archaeal methanogens and bacterial sulphate reducers, similar to those found in present-day anoxic marine sediments, may have already been in place at that time (Michaelis et al. 2002). As today, these consortia may have already included archaeal methanotrophs (Michaelis et al. 2002), since no anaerobic methane-oxidizing Bacteria are known (Chistoserdova et al. 2005). Both aerobic and anaerobic methanotrophy have been used to explain the highly depleted carbon isotopic values found in 2.8𠄲.6 Gyr geologic formations. Since oxygen would have still been a trace element in the atmosphere at the time, archaeal anaerobic methanotrophy is likely to have preceded bacterial aerobic methanotrophy.

The antiquity of archaeal fossil traces has been objected (Cavalier-Smith 2002) and possibly needs further confirmation. Moreover, the lack of reliable fossil traces for Archaea may severely affect any attempt to date the origin of this domain by molecular data. Hedges and colleagues recently estimated the divergence between Euryarchaeota and Crenarchaeota as old as 4.1 Gyr, but this was inferred by using the plant/animal divergence as a calibration point (Battistuzzi et al. 2004). The techniques to identify archaeal fossil traces in old samples should be developed further in the future and will provide reliable calibration points for the molecular dating of Archaea and prokaryotes in general.


Archaea and Evolution


The Archaea comprise a group of single-celled microorganisms that, like bacteria, are prokaryotes that have no cell nucleus or any other organelles within their cells. Consequently, they were once considered to be an unusual group of bacteria and named archaebacteria. However, it in now known that Archaeans have an independent evolutionary history and have numerous differences in their biochemistry compared to other forms of life. The differences are so great that they are now classified as a distinctly separate domain in the three-domain system. Carl Woese introduced the three main branches of evolutionary descent as the Archaea, Eukaryota and Bacteria. Classifying Archaea remains difficult, since the vast majority of these organisms have never been studied in the laboratory and have only been detected by analysis of their nucleic acids in environmental samples.

Archaeans are an ancient form of life, possibly the most ancient. Putative fossils of archaean cells in stromatolites have been dated to almost 3.5 billion years ago, and the remains of lipids that may be either archaean or eukaryotic have been detected in shales dating from 2.7 billion years ago. Since most prokaryotes do not have distinct morphologies, the shapes of fossils cannot be used to identify them as Archaea. Instead, chemical fossils, in the form of the unique lipids found in archaeans are used, and such lipids have now been detected in rocks dating back to the Archaean. The oldest known traces of these isoprene lipids have been found in Greenland, which include sediments formed 3.8 billion years old and are the oldest on Earth some scientists, however, dispute this claim.

The Theory of Endosymbiosis proposes that Eukaryotic life evolved from the Archaea. That is, the theory explains that organelles such as mitochondria and chloroplasts in eukaryotic cells evolved from certain types of bacteria that prokaryotic cells engulfed through endophagocytosis. These cells and the bacteria trapped inside subsequently evolved a symbiotic relationship. In this endosymbiotic relationship, the bacteria lived within the other prokaryotic cells.


Origins of DNA folding suggested in archaea

By studying the 3-D structure of proteins bound to DNA in microbes called archaea, researchers have turned up surprising similarities to DNA packing in more complicated organisms. "If you look at the nitty gritty, it's identical," says Howard Hughes Medical Institute Investigator Karolin Luger, a structural biologist and biochemist at the University of Colorado Boulder. "It just blows my mind."

The archaeal DNA folding, reported August 10 in Science, hints at the evolutionary origins of genome folding, a process that involves bending DNA and one that is remarkably conserved across all eukaryotes (organisms that have a defined nucleus surrounded by a membrane). Like Eukarya and Bacteria, Archaea represents one of the three domains of life. But Archaea is thought to include the closest living relatives to an ancient ancestor that first hit on the idea of folding DNA.

Scientists have long known that cells in all eukaryotes, from fish to trees to people, pack DNA in exactly the same way. DNA strands are wound around a "hockey puck" composed of eight histone proteins, forming what's called a nucleosome. Nucleosomes are strung together on a strand of DNA, forming a "beads on a string" structure. The universal conservation of this genetic necklace raises the question of its origin.

If all eukaryotes have the same DNA bending style, "then it must have evolved in a common ancestor," says study coauthor John Reeve, a microbiologist at Ohio State University. "But what that ancestor was, is a question no-one asked."

Earlier work by Reeve had turned up histone proteins in archaeal cells. But, archaea are prokaryotes (microorganisms without a defined nucleus), so it wasn't clear just what those histone proteins were doing. By examining the detailed structure of a crystal that contained DNA bound to archaeal histones, the new study reveals exactly how DNA packing works.

Luger and her colleagues wanted to make crystals of the histone-DNA complex in Methanothermus fervidus, a heat-loving archaeal species. Then, they wanted to bombard the crystals with X-rays. This technique, called X-ray crystallography, yields precise information about the position of each and every amino acid and nucleotide in the molecules being studied. But growing the crystals was tricky (the histones would stick to any given stretch of DNA, making it hard to create consistent histone-DNA structures), and making sense of the data they could get was no easy feat. "It was a very gnarly crystallographic problem," says Luger.

Yet Luger and her colleagues persisted. Postdoctoral researcher Sudipta Bhattacharyya "beat this thing with everything he could," says Luger, and ultimately solved the structure. The researchers revealed that despite using a single type of histone (and not four as do eukaryotes), the archaea were folding DNA in a very familiar way, creating the same sort of bends as those found in eukaryotic nucleosomes.

But there were differences, too. Instead of individual beads on a string, the archaeal DNA formed a long superhelix, a single, large curve of already twisty DNA strands. "In Archaea, you have one single building block," Luger says. "There is nothing to stop it. It's almost like it's a continuous nucleosome, really."

This superhelix formation, it turns out, is important. When postdoctoral researcher Francesca Mattiroli, together with the Santangelo lab, created mutations that interfered with this structure, the cells had trouble growing under stressful conditions. What's more, the cells seemed to not be using a set of their genes properly. "It's clear with these mutations that they can't form these stretches," says Mattiroli, of the University of Colorado Boulder.

The results suggest that the archaeal DNA folding is an early prototype of the eukaryotic nucleosome. "I don't think there's any doubt that it's ancestral," Reeve says.

Still, many questions remain. Luger says she'd like to look for the missing link -- a nucleosome-like structure that bridges the gap between the simple archaeal fold and the elaborate nucleosome found in eukaryotes, which can pack a huge amount of DNA into a small space and regulate gene behavior in many ways. "How did we get from here to there?" she asks.


22.1B: The Origins of Archaea and Bacteria - Biology

A headline on the front page of the New York Times for November 3, 1977, read “Scientists Discover a Way of Life That Predates Higher Organisms”. The accompanying article described a spectacular claim by Carl Woese and George Fox to have discovered a third form of life, a new ‘domain’ that we now call Archaea. It’s not that these microbes were unknown before, nor was it the case that their peculiarities had gone completely unnoticed. Indeed, Ralph Wolfe, in the same department at the University of Illinois as Woese, had already discovered how it was that methanogens (uniquely on the planet) make methane, and the bizarre adaptations that allow extremely halophilic archaea (then called halobacteria) and thermoacidophiles to live in the extreme environments where they do were already under investigation in many labs. But what Woese and Fox had found was that these organisms were related to each other not just in their ‘extremophily’ but also phylogenetically. And, most surprisingly, they were only remotely related to the rest of the prokaryotes, which we now call the domain Bacteria (Figure 1).


Archaea and CRISPR biology

The CRISPR-Cas system is an adaptive immune system encoded in prokaryotes to defend against invasion of foreign genetic elements. Current research data indicate that these immune systems are prevalent in Archaea, the third domain of life. Nevertheless, the prevalence probably reflects the fact that many of the current archaeal model organisms co-exist with a wide variety of viruses and are therefore enriched for the antiviral immunity. Furthermore, an additional layer of complexity of CRISPR mechanisms has recently been discovered, such that CRISPR functionality is further modulated by a widespread class of proteins named Cas accessory proteins. For this reason, these archaeal organisms provide unique resources for investigations to uncover the diversity and complexity of the immune system.

CRISPR-Cas as an anti-viral weapon in prokaryotes

Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated (Cas) system codes for an adaptive immunity in prokaryotes to defend against invasive genetic elements, including viruses and plasmids. The system is composed of CRISPR loci and cas gene cassettes. The former contain repetitive sequences that are interrupted by unique DNA sequences (spacers) derived from genetic elements, representing a memory of infection history of invasive genetic elements the latter code for proteins of RNA-binding, helicase and nuclease domains. The immune system functions in three distinct stages (Fig. 1): first, DNA segments in foreign genetic elements are acquired as new spacers in CRISPR loci (Adaptation) then, CRISPR loci are transcribed, yielding precursor CRISPR RNAs (pre-crRNAs) that are processed to produce mature crRNAs (Biogenesis) and finally, crRNAs guide Cas proteins to specifically target nucleic acids for destruction (Interference).

Antiviral immunity was first demonstrated for Streptococcus thermophilus, a lactic acid bacterium, in 2007. Upon the first exposure to a new bacteriophage, most bacterial cells are killed. However, a small portion of cells survive the bacteriophage infection and, commonly, one or more DNA fragments are gained from the bacteriophage genome and inserted into the chromosomal CRISPR loci of the host. Upon the re-occurrence of the phage infection the bacterium is then immune from the infection, and the immunity relies on the integrity of the CRISPR-Cas system. Investigation of many other CRISPR-Cas systems in archaea and bacteria has revealed that all systems studied function under the same principle. Further studies on CRISPR-Cas effector complexes containing crRNAs and Cas proteins have led to the illustration of molecular mechanisms of target DNA destruction for each type of CRISPR-Cas system.

Fig. 1. Basic mechanisms of the three-step antiviral pathway by CRISPR-Cas systems.

Striking diversity of CRISPR-Cas systems

The prevalence of the CRISPR-Cas system in prokaryotes allowed the identification of >45 families of Cas proteins in 2005, two years before the demonstration of CRISPR immunity. Most Cas proteins are not well conserved in amino acid sequence, but they form superfamilies of Cas proteins that are structurally and functionally related. Nevertheless, type-specific Cas proteins have been identified. In 2015, a major effort was made in the CRISPR community to classify CRISPR-Cas systems based on conservation of Cas proteins and the molecular mechanisms involved. This has yielded six main types of CRISPR-Cas systems, belonging to two main classes: those of Class 1 require multiple Cas proteins for interference whereas those of Class 2 use a single Cas protein for antiviral immunity. Each type of CRISPR-Cas system has a signature Cas protein, which is type-specific. For example, signature Cas proteins for the three classic types of CRISPR-Cas &ndash Types I, II and III &ndash are Cas3, Cas9 and Cas10, respectively. Furthermore, CRISPR-Cas systems are further divided into subtypes within each type. It is estimated that about 80% of archaea and about 40% of bacteria contain at least one CRISPR-Cas system. Since only a very small fraction of these prokaryotes are known, the diversity of CRISPR-Cas systems is much beyond our imagination. Indeed, a recent investigation by a metagenomic approach has led to the identification of several novel CRISPR-Cas systems.

In addition, some small archaeal plasmids carry a minimal CRISPR locus where no cas genes are identified. Nevertheless, spacers in the plasmid minimal CRISPR arrays match some viruses, suggesting that these plasmids could have developed a strategy to hijack the host CRISPR-Cas systems to silence virus infection.

The essence of uneven distribution of CRISPR-Cas systems in Archaea and Bacteria

The huge diversity of CRISPR-Cas systems raises a question as to how the systems evolve. In a CRISPR classification study, it was found that CRISPR-Cas systems show a biased distribution in Archaea and Bacteria. Whereas Type I CRISPR-Cas systems are abundant in both prokaryotic domains, all known Class 2 CRISPR-Cas systems are from bacteria, although some uncommon Class 2 systems are predicted in archaea, including a Type V system from the euryarchaeon &lsquoCandidatus Methanomethylophilus alvus&rsquo and two Type II systems from uncultivated nanoarchaea. On the other hand, archaea possess many more Type III systems than bacteria. Due to historical reasons, most known archaea belong to the so-called extremophiles in which CRISPR-Cas systems are prevalent. In particular, all known extremely thermophilic archaea carry more than one CRISPR-Cas system. The same is basically true for thermophilic bacteria. This suggests that CRISPR-Cas systems may have some additional functions that are important for certain physiological groups of organisms such as thermophiles. Interestingly, CRISPR-Cas systems are absent from Thaumarchaea and several bacterial taxa, further arguing for co-evolution between CRISPR-Cas systems and their archaeal and bacterial hosts. To this end, the apparent prevalence of CRISPR-Cas systems in archaea may reflect the fact that known archaea are dominated by those containing CRISPR-Cas systems. Possibly, more CRISPR-lacking phyla remain to be identified in Archaea.

Nevertheless, another possible reason accounting for the archaeal prevalence of CRISPR-Cas systems is the occurrence of highly diverse archaeal viruses that infect the archaeal model organisms. Therefore, the arms race between archaea and their diverse viruses may account for the presence of multiple diverse CRISPR-Cas systems in a single cell. In this respect, archaea and their CRISPR-Cas systems provide excellent resources for further studying CRISPR-Cas systems and their biological functions.

Cas accessory proteins as modulators of CRISPR functionality

The complexity of CRISPR biology has been further increased by the identification of a new class of CRISPR-related proteins termed &lsquoCas accessory proteins&rsquo. Their encoding genes are often clustered together with cas genes but they also appear in other genomic environments. Some of them are implicated in Adaptation while others, in Interference. They are probably not essential for the process of the three-step CRISPR immunity, but may modulate the functionality of the CRISPR-Cas system. Many of these proteins contain a CARF (CRISPR-associated Rossmann fold) domain, and they constitute the most abundant superfamily proteins associated with the CRISPR system. Cas accessory proteins belonging to the Csx1/Csm6 superfamily are probably among the most interesting ones. They are CARF domain ribonucleases, usually related to archaeal and bacterial Type III CRISPR-Cas systems that mediate transcription-dependent DNA interference. Since these systems require a cognate target RNA to activate the DNA interference, the CARF ribonuclease may modulate the CRISPR immunity by degrading viral transcripts. The mechanisms involved are one of the main focuses in CRISPR biology research, for which several archaea provide good models for investigation.

Development of CRISPR biotechnology

In 2012, Cas9-crRNA complexes were tested as a programmed endonuclease for genome editing, and the principle was soon applied in genome editing of human cell lines and mouse models. This method was termed as CRISPR technology simply because it was developed based on the CRISPR immune principle. To date, the technology has been further developed to extend the application to transcription regulation, genome imaging and epigenetic regulation. The application can also be on a genome-wide scale to assay gene functions. Focused research in CRISPR biology and biotechnology will greatly increase our understanding of these unique, prokaryotic adaptive immune systems, and facilitate CRISPR applications for years to come.

Qunxin She & Wenyuan Han

University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
[email protected]
[email protected]

Further reading

Burstein, D. & others (2017). New CRISPR- Cas systems from uncultivated microbes. Nature 542, 237&ndash241.

Makarova, K. S. & others (2015). An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol 13, 722&ndash736.

Mohanraju, P. & others (2016). Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science 353, aad5147.

Tamulaitis, G. & others (2017). Type III CRISPR-Cas Immunity: Major Differences Brushed Aside. Trends Microbiol 25, 49&ndash61.

Images: Fig. 1. Jennifer Doudna, HHMI/UC Berkeley. Computer model showing the CRISPR-Cas silencing Cmr subunits bound to RNA (cyan) and DNA (red). A number of Cmr atoms have been removed in order to show RNA and DNA. Laguna Design/Science Photo Library.


Microbial Biodiversity

Kristin L. Matulich , . Jennifer B.H. Martiny , in Encyclopedia of Biodiversity (Second Edition) , 2013

Glossary

One of the two entirely microbial domains of single-celled organisms, evolutionarily distinct from bacteria. Many archaeal characteristics are more similar to eukaryotes than bacteria.

An entirely microbial domain of single-celled organisms, evolutionarily distinct from Archaea.

A primarily microbial domain of organisms having a membrane-enclosed nucleus and other organelles includes animals, plants, fungi, and protists.

Nonphototrophic, heterotrophic eukaryotic microorganisms that contain rigid cell walls includes mushrooms, molds, and the fungal part of lichens.

The genomic analysis of microorganisms by direct extraction and cloning of community deoxy ribonucleic acid (DNA) from an environmental sample.

Single-celled organisms that can only be observed with a microscope, including bacteria, archaea, small eukaryotes, and viruses.

Operational taxonomic unit (OTU)

A group of organisms regarded as being distinct from other groups, based on any clearly defined variables.

Polymerase chain reaction (PCR)

A method for copying DNA sequences by repeated cycles of synthesis using specific primers and DNA polymerase.

A genetic element containing either DNA or ribonucleic acid (RNA) that replicates in cells but is characterized by having an extracellular state.



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