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Eukaryotic Origins* - Biology

Eukaryotic Origins* - Biology


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Eukaryotes

Living things fall into three large groups:Archaea, Bacteria, and Eukarya. The first two groups include non-nucleated cells, and the third contains all eukaryotes. A relatively sparse fossil record is available to help us discern what the first members of each of these lineages looked like, so it is possible that all the events that led up to the last common ancestor of extant eukaryotes will remain unknown. However, comparative biology of extant organisms and the limited fossil record provide some insights into the history of Eukarya.

The earliest fossils found appear to be bacteria, most likely cyanobacteria. They are about 3.5 billion years old and are recognizable because of their relatively complex structure and, for bacteria, relatively large cells. Most other bacteria and archaea have small cells, 1 or 2µmin size, and would be difficult to pick out as fossils. Most living eukaryotes have cells measuring 10µmor greater. Structures this size, which might be fossils, appear in the geological record about 2.1 billion years ago.

Characteristics of eukaryotes

Data from these fossils have led biologists to the conclusion that living eukaryotes are all descendants of a single common ancestor. Mapping the characteristics found in all major groups of eukaryotes reveals that the following characteristics must have been present in the last common ancestor, because these characteristics are present in at leastsome of themembers of each major lineage.

  1. Cells with nuclei surrounded by a nuclear envelope with nuclear pores. This is the single characteristic that is both necessary and sufficient to define an organism asaeukaryote. All extant eukaryotes have cells with nuclei.
  2. Mitochondria. Some extant eukaryotes have very reduced remnants of mitochondria in their cells, whereas other members of their lineages have “typical” mitochondria.
  3. A cytoskeleton containing the structural and motility components calledactinmicrofilaments and microtubules. All extant eukaryotes have these cytoskeletal elements.
  4. Flagella and cilia, organelles associated with cell motility. Some extant eukaryotes lack flagella and/or cilia, butthey are descendedfrom ancestors that possessed them.
  5. Chromosomes, eachconsisting ofa linear DNA molecule coiled around basic (alkaline) proteins called histones. The few eukaryotes with chromosomes lacking histonesclearlyevolved from ancestors that had them.
  6. Mitosis, a process of nuclear division wherein replicated chromosomesare dividedand separated using elements of the cytoskeleton. Mitosis is universally present in eukaryotes.
  7. Sex, a process of genetic recombination unique to eukaryotes in which diploid nuclei at one stage of the life cycle undergo meiosis to yield haploid nuclei and subsequent karyogamy, a stage where two haploid nuclei fusetogetherto create a diploid zygote nucleus.
  8. Members of all major lineages have cell walls, and it might be reasonable to conclude that the last common ancestor could make cell walls during some stage of its life cycle. However, not enoughis knownabout eukaryotes’ cell walls and their development to know how much homology exists among them. If the last common ancestor could make cell walls,it is clear thatthis ability must have been lostin many groups.

Endosymbiosis and the evolution of eukaryotes

In order tounderstand eukaryotic organisms fully, it is necessary to understand that all extant eukaryotes are descendants of a chimeric organism that was a composite of a host cell and the cell(s) of an alpha-proteobacteriumthat “took up residence” inside it.This major theme in the origin ofeukaryotesis knownas endosymbiosis, one cell engulfing another such that the engulfed cell survives and both cells benefit. Over many generations, a symbiotic relationship canresult intwo organisms that depend on each other so completely that neither could survive on its own.Endosymbioticevents likely contributed to the origin of the last common ancestor of today’s eukaryotes and to later diversification in certain lineages of eukaryotes. Before explaining this further, it is necessary to consider metabolism in bacteria and archaea.

Bacterial and archaeal metabolism

Many important metabolic processes arose in bacteria and archaea, and some of these, such as nitrogen fixation,are never foundin eukaryotes. The process of aerobic respirationis foundin all major lineages of eukaryotes, andit is localizedin the mitochondria.Aerobic respiration is also foundin many lineages of bacteria and archaea, but it is not present in all of them, and many forms of evidence suggest that such anaerobic microbes never carried out aerobic respiration nor did their ancestors.

While today’s atmosphere is about one-fifth molecular oxygen (O2), geological evidence shows that it originally lacked O2. Without oxygen, aerobic respiration would notbe expected, and living things would have relied on fermentation instead. Around 3.5 billion years ago, some bacteria and archaea began using energy from sunlight to power anabolic processes that reduce carbon dioxide to form organic compounds. They evolved the ability to photosynthesize. Hydrogen, derived from various sources,was capturedusing light-powered reactions to reduce fixed carbon dioxide in the Calvin cycle. The group of Gram-negative bacteria that gave rise to cyanobacteria used water as the hydrogen source and released O2 as a waste product.

Eventually, the amount of photosynthetic oxygen built up in some environments to levels that posed a risk to living organisms, since it can damage many organic compounds. Various metabolic processes evolved that protected organisms from oxygen; one of which, aerobic respiration, also generated high levels of ATP. It became widely present among microbes, including in a group we now call alpha-proteobacteria. Organisms that did not gain aerobic respiration had to remain in oxygen-free environments. Originally, oxygen-rich environments were likely localized around places where cyanobacteria were active, but by about 2 billion years ago, geological evidence shows that oxygen was building up to higher concentrations in the atmosphere. Oxygen levels similar to today’s levels only arose within the last 700 million years.

Recall that the first fossils that we believe to be eukaryotes are about 2 billion years old, so they appeared as oxygen levels were increasing. Also, recall that all extant eukaryotes descended from an ancestor with mitochondria. These organelles were first observed by light microscopists in the late 1800s, where they appeared to be worm-shaped structures that seemed to move around in the cell. Some early observers suggested that they might be bacteria living inside host cells, but these hypotheses remained unknown or rejected in most scientific communities.

Endosymbiotictheory

As cell biology developed in the twentieth century,it became clear thatmitochondria were the organelles responsible for producing ATP using aerobic respiration. In the 1960s, American biologist Lynn Margulis developed endosymbiotictheory, which states that eukaryotes may have been a product of one cell engulfing another (one living within another) and evolving until the separate cells were no longer recognizableas such. In 1967, Margulis introduced new work on the theory and substantiated her findings through microbiological evidence. Although Margulis’ work initiallywas metwith resistance, this once-revolutionary hypothesis is now widely (but not completely) accepted, with work progressing on uncovering the steps involved in this evolutionary process and the key players involved. Much remains tobe discoveredabout the origins of the cells that now make up the cells in all living eukaryotes.

Broadly, it has become clear that many of our nuclear genes and the molecular machinery responsible for replication and expression appear closely related to those inArchaea.On the other hand, themetabolic organelles and genes responsible formany energy-harvesting processes had their origins in bacteria. Much remains tobe clarifiedabout how this relationship occurred; this continues to be an exciting field of discovery in biology. For instance, itis not knownwhether the endosymbiotic event that led to mitochondria occurred before or after the host cell had a nucleus. Such organisms would be among the extinct precursors of the last common ancestor of eukaryotes.

Mitochondria

One of the major features distinguishing bacteria and archaea from eukaryotes is mitochondria. Eukaryotic cells may contain anywhere from one to several thousand mitochondria, depending on the cell’s level of energy consumption. Each mitochondrion measures 1 to 10 or greater micrometersin lengthand exists in the cell as an organelle that can be ovoid, worm-shaped, or intricately branched. Mitochondria arise from the division of existing mitochondria; they may fuse; andthey may be movedaround inside the cell by interactions with the cytoskeleton. However, mitochondria cannot survive outside the cell. As the atmospherewas oxygenatedby photosynthesis, and as successful aerobic microbes evolved, evidence suggests that an ancestral cell with some membrane compartmentalization engulfed a free-living aerobic bacterium, specifically an alpha-proteobacterium,therebygiving the host cell the ability to use oxygen to release energy stored in nutrients. Alpha-proteobacteriaare a large group of bacteria that includes species symbiotic with plants, disease organisms that can infect humans via ticks, and many free-living species that use light for energy. Several lines of evidence support that mitochondriaare derivedfrom this endosymbiotic event. Most mitochondriaare shapedlike alpha-proteobacteriaandare surroundedby two membranes, which would result when one membrane-bound organismis engulfedinto a vacuole by another membrane-bound organism. The mitochondrial inner membrane is extensive and involves substantialinfoldingscalled cristae that resemble the textured, outer surface of alpha-proteobacteria. The matrix and inner membrane are rich with the enzymes necessary for aerobic respiration.


Section Summary

The oldest fossil evidence of eukaryotes is about 2 billion years old. Fossils older than this all appear to be prokaryotes. It is probable that today’s eukaryotes are descended from an ancestor that had a prokaryotic organization. The last common ancestor of today’s Eukarya had several characteristics, including cells with nuclei that divided mitotically and contained linear chromosomes where the DNA was associated with histones, a cytoskeleton and endomembrane system, and the ability to make cilia/flagella during at least part of its life cycle. It was aerobic because it had mitochondria that were the result of an aerobic alpha-proteobacterium that lived inside a host cell. Whether this host had a nucleus at the time of the initial symbiosis remains unknown. The last common ancestor may have had a cell wall for at least part of its life cycle, but more data are needed to confirm this hypothesis. Today’s eukaryotes are very diverse in their shapes, organization, life cycles, and number of cells per individual.


Eukaryotic Origins* - Biology

The cell membrane is a fundamental and defining feature of cells. The realization that the 3 domains of life: Bacteria, Archaea and Eukarya, have distinct membrane lipid compositions poses challenges and offers hints to reconstructing the evolutionary history of life on Earth.

The origin of eukaryotic cells is deeply puzzling, because even a superficial comparison of eukaryotic cells with prokaryotic cells reveals many complex innovations that seemingly arose all at once. However, new and recent discoveries have revealed possible origins for some of these eukaryotic features in some groups of prokaryotes.

Shortly after the discovery and characterization of Archaea as an entirely new domain of life, separate from Bacteria and Eukarya, molecular phylogeny based on ribosomal RNA suggested that Archaea and Eukarya have a more recent common ancestor than Archaea and Bacteria, or Eukarya and Bacteria. Indeed, Archaea and Eukarya have many genetic similarities. RNA polymerase, histone-like proteins, DNA polymerase are a few key examples (see review by Allers and Mevarech, 2005). However, many other genes in eukaryotes appear to be more similar to their bacterial homologues than to the Archaeal versions. The presence of both Archaeal and Bacterial genes in eukaryotic genomes have led to a number of hypotheses postulating various mash-ups between Bacteria and Archaea as a key originating event for eukaryotic evolution, with most favoring Archaea as a source of nuclear processes and Bacteria for cytoplasmic and metabolic processes (Cotton and McInerney, 2010).

Archaeal taxonomy, from Allers and Mevarech, Nature Reviews Genetics 6: 58-73

Some recent papers have focused attention on membrane lipids and membrane processes. Archaea have utterly different membrane lipid composition, with isoprenoid chains instead of fatty acids, L-glycerol instead of D-glycerol, and ether linkages instead of ester linkages (see http://www.ucmp.berkeley.edu/archaea/archaeamm.html and http://en.wikipedia.org/wiki/Archaea). Bacteria and Eukarya both have the familiar membrane phospholipids with esterified fatty acyl chains.

Ether-linked phospholipids in Archaea, compared with ester-linked phospholipids. Image from http://www.ucmp.berkeley.edu/archaea/archaeamm.html

Any hypothesis about the origin of eukaryotic cells must reconcile the archaeal characteristics of the eukaryotic information processing genes, against the absence of Archaeal characteristics from the eukaryotic membrane.

Eukaryotes also have membrane innovations that are not found in either Archaea or Bacteria: sterols and sphingolipids. Sterols (like cholesterol) and sphingolipids are important components of eukaryotic plasma membranes, and together can constitute 50% of the lipids of the outer leaflet (Desmond and Gribaldo, 2009 sphingolipids are not found in the cytoplasmic side of the plasma membrane lipid bilayer). Sterols are essential components of all eukaryotic cell membranes. They modulate membrane fluidity and permeability. Together with sphingolipids they help organize regions of the membrane into lipid rafts, microdomains in the plasma membrane with reduced fluidity, that organize cell signaling proteins into functional complexes (see review by Lingwood and Simons, 2010).

Sterol biosynthesis is a complex pathway that requires molecular oxygen (11 molecules of oxygen are required to synthesize just one molecule of cholesterol) (Desmond and Gribaldo, 2009). Therefore, steroid biosynthesis could not have evolved before the Great Oxygenation Event, circa 2.4-2.5 billion years ago. Significantly, this time coincides with the origin of eukaryotes. Evolution of steroid biosynthesis pathways thus looks like one of the keys to evolution of eukaryotes.

A recent phylogenomic analysis (Desmond and Gribaldo 2009) inferred that the last eukaryotic common ancestor had a suite of enzymes for synthesis of a diverse array of sterols. Intriguingly, a few bacterial lineages also synthesize sterols, and their genomes contain homologs of the genes for key sterol biosynthesis enzymes. The question is whether:

1) these bacteria acquired these genes from eukaryotes, via lateral gene transfer (also called horizontal gene transfer), or

2) these genes are cousins to the eukaryotic sterol synthesis genes, descendants of genes present in a common ancestor of these bacteria and eukaryotes, or

3) these genes evolved independently in these bacteria, and similarities to eukaryotic genes arose by convergent evolution.

The last possibility seems quite implausible, given that there are multiple genes. Indeed the phylogenetic trees are consistent with two of the genes for the first steps in sterol biosynthesis sorting into distinct bacterial and eukaryotic lineages (see Desmond and Gribaldo, Fig. 6, shown below).

Desmond and Gribaldo 2009 Fig. 6. Erg1 genes from bacteria form a distanct group from the eukaryotic Erg1 genes

These results are consistent with either hypothesis 2) above, or lateral gene transfer very early in eukaryotic evolution. Other bacterial sterol synthesis genes such as Erg7 clearly appear to have been acquired more than once from eukaryotes via lateral gene transfer, because these gene sequences appear in clusters with eukaryotic Erg7 gene sequences (Desmond and Gribaldo 2009 Fig. 8).

Desmond and Gribaldo 2009 Fig. 8. Erg7 in bacteria appears in a cluster with eukaryotic Erg7 genes

Do these findings then suggest that the eukaryotic cell membrane is descended or borrowed from Bacteria? Was the eukaryotic ancestor a bacterium that captured an Archaeon, with the Archaeon subsequently evolving into the nucleus? If, instead, an Archaeon was host to bacteria that became mitochondria, why would the cell membrane become bacterial instead of retaining Archaeal lipids? Time, and analyses of a greater diversity of genomes, may tell.

Allers, T, M Mevarech 2005. Archaeal genetics – the third way, Nature Reviews Genetics 6: 58-73 doi :10.1038/nrg1504

Cotton, JA, JO McInerney 2010. Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function, Proc. Natl. Acad Sci. USA published online before print doi: 10.1073/pnas.1000265107

Desmond, E, S Gribaldo 2009. Phylogenomics of sterol synthesis: insights into the origin, evolution, and diversity of a key eukaryotic feature, Genome Biol Evol 1: 364-381 doi: 10.1093/gbe/evp036

Lingwood, D, K Simons 2010. Lipid rafts as a membrane-organizing principle, Science 327: 46-50

Lonhienne, TGA, E Sagulenko, RI Webb, K-C Lee, J Franke, DP Devos, A Nouwens, BJ Carroll, JA Fuerst 2010. Endocytosis-like protein uptake in the bacterium Gemmata obscuriglobus, Proc. Natl. Acad Sci. USA published online before print doi: 10.1073/pnas.1001085107


Endosymbiotic theories for eukaryote origin

For over 100 years, endosymbiotic theories have figured in thoughts about the differences between prokaryotic and eukaryotic cells. More than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. Very few of those models account for eukaryotic anaerobes. The role of energy and the energetic constraints that prokaryotic cell organization placed on evolutionary innovation in cell history has recently come to bear on endosymbiotic theory. Only cells that possessed mitochondria had the bioenergetic means to attain eukaryotic cell complexity, which is why there are no true intermediates in the prokaryote-to-eukaryote transition. Current versions of endosymbiotic theory have it that the host was an archaeon (an archaebacterium), not a eukaryote. Hence the evolutionary history and biology of archaea increasingly comes to bear on eukaryotic origins, more than ever before. Here, we have compiled a survey of endosymbiotic theories for the origin of eukaryotes and mitochondria, and for the origin of the eukaryotic nucleus, summarizing the essentials of each and contrasting some of their predictions to the observations. A new aspect of endosymbiosis in eukaryote evolution comes into focus from these considerations: the host for the origin of plastids was a facultative anaerobe.

Keywords: anaerobes endosymbiosis eukaryotes mitochondria nucleus plastids.

Figures

Models describing the origin of…

Models describing the origin of the nucleus in eukaryotes. ( ao…

Models describing the origin of…

Models describing the origin of mitochondria and/or chloroplasts in eukaryotes. ( a –…

Mitochondrial origin in a prokaryotic…

Mitochondrial origin in a prokaryotic host. ( ah ) Illustrations for…

Evolution of anaerobes and the…

Evolution of anaerobes and the plastid. ( ad ) Diversification of…


3. The endosymbiotic origin of the chloroplast

During phagocytosis in white blood cells or many protozoa (Figure 5), ingested cells are often directly digested (as in the case of prey), but sometimes they are permanently lodged in the cells (endosymbiotes). In the endosymbiosis process, organelle therefore results from internalization by phagocytosis without digestion of a prokaryote within a eukaryote (Figure 5). This is the case for chloroplasts in terrestrial plants, but also for red and green algae that are close to them [11,12].

Figure 5. Phagocytosis and primary endosymbiosis. During phagocytosis, ingested prey is often directly digested, but sometimes permanently lodged in the cells during primary endosymbiosis, the plasma membrane of the cell invades around the prokaryote and isolates it within an endocytosis vesicle. Then, when the prokaryote is integrated into the eukaryotic cell, the membrane of this vesicle disappears as well as the layer of peptidoglycans located between the two membranes of the cyanobacterium [see ref. 9 & 10]. During phagocytosis processes, the plasma membrane of the cell invades around the prey and isolates them into endocytosis vesicles where they are then digested as these vesicles fuse with others, the lysosomes, which contain enzymes. By analogy, it was generally considered that the outer membrane of the organelles came from this endocytosis membrane. Things are likely to be more complex (Figure 5). Indeed, the prokaryotes at the origin of chloroplasts or mitochondria are Gram- bacteria, characterized by the existence of a double membrane on the periphery of the bacteria. The outer membrane of chloroplasts, and in particular its outer surface immersed in the cell’s cytosol, contains characteristic glycolipids found in cyanobacteria [9, 10, 13] . It is therefore possible that the endocytosis membrane may have disappeared during the integration of the prokaryote into the eukaryotic cell. This is currently observed in Elysia chlorotica (see Focus), a marine mollusc that grazes algae, digests part of their cells but not the chloroplasts which is integrated into the cytoplasm of some of its cells. These chloroplasts remain functional throughout the life of the mollusc, which benefits from photosynthesis.

Primary and secondary endosymbioses
During the evolution, several endosymbiosis events repeated themselves and led to the formation of particular organisms. In primary endosymbiosis, the eukaryotic cell integrates a living prokaryotic. Thus, the chloroplasts of green line plants (red and green algae, to which terrestrial plants are attached) are derived from primary endosymbioses involving cyanobacteria. In some eukaryotes, mitochondria have evolved as a result of adaptation to anaerobic environments, but have never disappeared: they have produced particular mitochondria ( hydrogenosomes Organelles producing hydrogen, derived from a mitochondria. It is found in some anaerobic ciliates, Trichomonas, and fungi. ) carrying out H2-producing fermentation (for example in some Ciliates) [14], but also small organelles, only involved in biosynthesis for the host cell, the mitosomes Organelles present in some single-celled eukaryotic organisms, probably lacking DNA but with biosynthesis functions. [15].

Figure 6. Secondary chloroplastic endosymbiosis model in the cryptophyte Guillardia theta [see ref. 18]. Here, the nucleus of the internalised red algae (primary host) persists within the secondary host in the form of a vestigial nucleus (or nucleomorph), but with a very small genome (551 kb instead of the 350 Mb of the nucleus). Secondary endosymbioses are a reiteration of the process, when a eukaryote already containing an endosymbiont realizes a secondary endosymbiosis within another eukaryote (Figure 6). This is the origin of plastids with more than two membranes present in some groups: internalisation of a green algae in Euglenes independent internalisation of a red algae in brown algae, etc. Tertiary endosymbiosis, less frequent, have also been described. These various symbioses constitute as many founding endosymbioses of evolutionary lines [16,17].


Eukaryotic Origins* - Biology

Unit Four. The Evolution and Diversity of Life

17. Protists: Advent of the Eukaryotes

You are a eukaryote, an organism composed of cells that contain a nucleus. All the organisms you see around you are eukaryotes, too, as prokaryote organisms are too small for you to see without a microscope to magnify them. Biologists sort the eukaryotes of the living world into four great groups, called kingdoms: animals, plants, fungi, and everything else. This chapter concerns the fourth catch-all group, the protists (kingdom Protista). The beautiful flowerlike creature you see here is a protist, the green algae Acetabularia. It is photosynthetic and grows as long slender stalks as long as your thumb. In the last century some biologists considered it to be a very simple sort of plant. Today, however, most biologists consider Acetabularia to be a protist, restricting the plant kingdom to multicellular terrestrial photosynthetic organisms (and a few marine and aquatic species like water lilies clearly derived from terrestrial ancestors). Acetabularia is marine, not terrestrial, and it is unicellular, with a single nucleus found in the base of its stalk. In this chapter, we will explore how protists are thought to have evolved, and the sorts of creatures found among this most diverse of biological kingdoms. Multicellularity evolved many times within the protists, producing the ancestors of the animal, plant, and fungi kingdoms, as well as several kinds of multicellular algae, some as large as trees.

17.1. Origin of Eukaryotic Cells

The First Eukaryotic Cells

All fossils more than 1.7 billion years old are small, simple cells, similar to the bacteria of today. In rocks about 1.7 billion years old, we begin to see the first microfossils, which are noticeably larger than bacteria and have internal membranes and thicker walls. A new kind of organism had appeared, called a eukaryote (Greek eu, “true,” and karyon, “nut”). One of the main features of a eukaryotic cell is the presence of an internal structure called a nucleus (see section 4.5). As discussed in chapter 15, animals, plants, fungi, and protists are all eukaryotes. In this chapter, we will explore the protists, from which all other eukaryotes evolved. But first we will examine some of the unifying characteristics of eukaryotes, and how they might have originated.

To begin, how might a nucleus have arisen? Many bacteria have infoldings of their outer membranes extending into the interior that serve as passageways between the surface and the cell’s interior. The network of internal membranes in eukaryotes, called the endoplasmic reticulum (ER), is thought to have evolved from such infoldings, as is the nuclear envelope (figure 17.1). The prokaryotic cell shown on the far left has infoldings of the plasma membrane, and the DNA resides in the center of the cell. In ancestral eukaryotic cells, these internal membrane extensions evolved to project farther into the cell, continuing their function as passageways between the interior and exterior of the cell. Eventually, these membranes came to form an enclosure surrounding the DNA, shown on the right, which became the nuclear envelope.

Figure 17.1. Origin of the nucleus and endoplasmic reticulum.

Many bacteria today have infoldings of the plasma membrane. The eukaryotic internal membrane system called the endoplasmic reticulum (ER) and the nuclear envelope may have evolved from such infoldings of the plasma membrane of prokaryotic cells that gave rise to eukaryotic cells.

What was the first eukaryote like? We cannot be sure, but a good model is Pelomyxa palustris, a single-celled, nonphotosynthetic organism that some scientists feel represents an early stage in the evolution of eukaryotic cells. The cells of Pelomyxa are much larger than bacterial cells and contain a complex system of internal membranes. Although they resemble some of the largest early fossil eukaryotes, these cells are unlike those of any other eukaryote: Pelomyxa lacks mitochondria and only rarely undergoes mitosis. However, biologists know very little of the origin of Pelomyxa. It may have lost mitochondria rather than never having had them at all. This primitive eukaryote is so distinctive that it is assigned a phylum all its own, Caryoblastea.

Because of similarities in their DNA, it is widely assumed that the first eukaryotic cells were nonphotosynthetic descendants of archaea.

In addition to an internal system of membranes and a nucleus, eukaryotic cells contain several other distinctive organelles. These organelles were discussed in chapter 4. Two of these organelles, mitochondria and chloroplasts, are especially unique because they resemble bacterial cells and even contain their own DNA. As discussed in section 4.7 and section 15.9, mitochondria and chloroplasts are thought to have arisen by endosymbiosis, where one organism comes to live inside another. The endosymbiotic theory, now widely accepted, suggests that at a critical stage in the evolution of eukaryotic cells, energy-producing aerobic bacteria came to reside symbiotically (that is, cooperatively) within larger early eukaryotic cells, eventually evolving into the cell organelles we now know as mitochondria. Similarly, photosynthetic bacteria came to live within some of these early eukaryotic cells, leading to the evolution of chloroplasts (figure 17.2), the photosynthetic organelles of plants and algae. Now, let’s examine the evidence supporting the endosymbiotic theory a little more closely.

Figure 17.2. The theory of endosymbiosis.

Scientists propose that ancestral eukaryotic cells engulfed aerobic bacteria, which then became mitochondria in the eukaryotic cell. Chloroplasts may also have originated in this way, with eukaryotic cells engulfing photosynthetic bacteria that became chloroplasts.

Mitochondria. Mitochondria, the energy-generating organelles in eukaryotic cells, are sausage-shaped organelles about 1 to 3 micrometers long, about the same size as most bacteria. Mitochondria are bounded by two membranes. The outer membrane is smooth and was apparently derived from the host cell as it wrapped around the bacterium. The inner membrane is folded into numerous layers, embedded within which are the proteins of oxidative metabolism.

During the billion-and-a-half years in which mitochondria have existed as endosymbionts within eukaryotic cells, most of their genes have been transferred to the chromosomes of the host cells—but not all. Each mitochondrion still has its own genome, a circular, closed molecule of DNA similar to that found in bacteria, on which is located genes encoding some of the essential proteins of oxidative metabolism. These genes are transcribed within the mitochondrion, using mitochondrial ribosomes that are smaller than those of eukaryotic cells, very much like bacterial ribosomes in size and structure. Mitochondria divide by simple fission, just as bacteria do, and can divide on their own without the cell nucleus dividing. Mitochondria also replicate and sort their DNA much as bacteria do. However, the cell’s nuclear genes direct the process, and mitochondria cannot be grown outside of the eukaryotic cell, in cell-free culture.

Chloroplasts. Many eukaryotic cells contain other endosymbi- otic bacteria in addition to mitochondria. Plants and algae contain chloroplasts, bacteria-like organelles that were apparently derived from symbiotic photosynthetic bacteria. Chloroplasts have a complex system of inner membranes and a circle of DNA. While all mitochondria are thought to have arisen from a single symbiotic event, it is difficult to be sure with chloroplasts. Three biochemically distinct classes of chloroplasts exist, but all appear to have their origin in the cyanobacteria.

Red algae and green algae seem to have acquired cyanobacteria directly as endosymbionts, and may be sister groups. Other algae have chloroplasts of secondary origin, having taken up one of these algae in their past. The chloroplasts of euglenoids are thought to be green algal in origin, while those of brown algae and diatoms are likely of red algal origin. The chloroplasts of dinoflagellates seem to be of complex origins, which might include diatoms.

As mentioned earlier, the primitive eukaryote Pelomyxa does not exhibit mitosis, the eukaryotic process of cell division. How did mitosis evolve? The mechanism of mitosis, now so common among eukaryotes, did not evolve all at once. Traces of very different, and possibly intermediate, mechanisms survive today in some of the eukaryotes. In fungi and some groups of protists, for example, the nuclear membrane does not dissolve, and mitosis is confined to the nucleus. When mitosis is complete in these organisms, the nucleus divides into two daughter nuclei, and only then does the rest of the cell divide. This separate nuclear division phase of mitosis does not occur in most protists, or in plants or animals. We do not know if it represents an intermediate step on the evolutionary journey to the form of mitosis that is characteristic of most eukaryotes today, or if it is simply a different way of solving the same problem. There are no fossils in which we can see the interiors of dividing cells well enough to be able to trace the history of mitosis.

Key Learning Outcome 17.1. The theory of endosymbiosis proposes that mitochondria originated as symbiotic aerobic bacteria and chloroplasts originated from a second endosymbiotic event with photosynthetic bacteria.


For Students & Teachers

For Teachers Only

ENDURING UNDERSTANDING

EVO-1
Evolution is characterized by a change in the genetic makeup of a population over time and is supported by multiple lines of evidence.

LEARNING OBJECTIVE

EVO-1.A
Describe similarities and/or differences in compartmentalization between prokaryotic and eukaryotic cells.

EVO-1.B
Describe the relationship between the functions of endosymbiotic organelles and their free-living ancestral counterparts.

ESSENTIAL KNOWLEDGE

EVO-1.A.1
Membrane-bound organelles evolved from once free-living prokaryotic cells via endosymbiosis.

EVO-1.A.2
Prokaryotes generally lack internal membrane-bound organelles but have internal regions with specialized structures and functions.

EVO-1.A.3
Eukaryotic cells maintain internal membranes that partition the cell into specialized regions.

EVO-1.B.1
Membrane-bound organelles evolved from previously free-living prokaryotic cells via endosymbiosis.


Virus Replication

Jennifer Louten , in Essential Human Virology , 2016

4.4.1 Class I: dsDNA Viruses

All living organisms have double-stranded DNA genomes. Viruses with dsDNA genomes therefore have the most similar nucleic acid to living organisms and often use the enzymes and proteins that the cell normally uses for DNA replication and transcription, including its DNA polymerases and RNA polymerases. These are located in the nucleus of a eukaryotic cell, and so all dsDNA viruses that infect humans (with the exception of poxviruses) enter the nucleus of the cell, using the various mechanisms of entry and uncoating mentioned above. Many recognizable human viruses have dsDNA genomes, including herpesviruses, poxviruses, adenoviruses, and polyomaviruses.

Transcription of viral mRNA (vmRNA) must occur before genome replication if viral proteins are involved in replicating the virus genome. In addition, certain translated viral proteins act as transcription factors to direct the transcription of other genes. As discussed in Chapter 3, “Features of Host Cells: Cellular and Molecular Biology Review , transcription factors bind to specific sequences within the promoters of cellular genes immediately upstream of the transcription start site to initiate transcription of those genes. Enhancers, regulatory sequences also involved in transcription, are located farther away from the transcription start site and can be upstream or downstream. dsDNA viruses also have promoter and enhancer regions within their genomes that are recognized not only by viral transcription factors but by host transcription factors, as well. These proteins initiate transcription of the viral genes by the host RNA polymerase II.

Processing of viral precursor mRNA (also known as posttranscriptional modification) occurs through the same mechanisms as for cellular mRNA. Viral transcripts receive a 5′-cap and 3′-poly(A) tail, and some viruses’ transcripts are spliced to form different vmRNAs. For example, the genes of herpesviruses are each encoded by their own promoter and are generally not spliced, but the human adenovirus E genome has 17 genes that encode 38 different proteins, derived by alternative splicing of vmRNA during RNA processing.

The dsDNA viruses transcribe their viral gene products in waves, and the immediate early and/or early genes are the first viral genes to be transcribed and translated into viral proteins. These gene products have a variety of functions, many of which help to direct the efficient replication of the genome and further transcription of the late genes that encode the major virion structural proteins and other proteins involved in assembly, maturation, and release from the cell. The replication of the viral genome requires many cellular proteins having the late genes transcribed and translated after the virus genome has been replicated ensures that the host enzymes needed for replication are not negatively affected by the translation of massive amount of virion structural proteins.

To create new virions, viral proteins must be translated and the genome must also be copied. With the exception of poxviruses, the genome replication of all dsDNA viruses takes place within the nucleus of the infected cell. Eukaryotic DNA replication , also reviewed in more detail in Chapter 3, “Features of Host Cells: Cellular and Molecular Biology Review,” is also carried out by DNA polymerases and other proteins within the nucleus. DNA polymerases, whether they are cell derived or virus derived, cannot carry out de novo synthesis, however. They must bind to a short primer of nucleic acid that has bound to the single-stranded piece of DNA, forming a short double-stranded portion that is then extended by DNA polymerase ( Fig. 4.8A ). Primase is the enzyme that creates primers during cellular DNA replication, and some viruses, such as polyomaviruses and some herpesviruses, take advantage of the cellular primase enzyme to create primers on their dsDNA genomes during replication. Other herpesviruses, such as HSV-1, provide their own primase molecule, although this process occurs less commonly. Still other viruses, such as the adenoviruses, encode a viral protein primer that primes its own viral DNA polymerase ( Fig. 4.8B ). Cellular DNA polymerases are used by polyomaviruses and papillomaviruses, while all other dsDNA viruses encode their own DNA polymerases to replicate the viral genome. Many other cellular enzymes and proteins are required for DNA synthesis, and viruses are dependent on these to varying degrees, depending upon the specific virus. The poxviruses are a notable exception to this: they encode all the proteins necessary for DNA replication. In fact, they also encode the proteins needed for transcription of RNA, and so, unlike all other dsDNA viruses, they do not need to gain entry into the nucleus of a host cell for either genome replication or transcription and processing of viral genes, allowing their replication to take place entirely in the cytoplasm.

DNA polymerases cannot carry out de novo synthesis and so need a primer in order to replicate DNA. Some viruses take advantage of the cellular primase in order to create primers (A), while other viruses, such as adenoviruses, encode a protein primer that primes its own DNA polymerase (B). In the process of self-priming, the ssDNA genomes of parvoviruses fold back upon themselves to form hairpin ends that act as a primer for host DNA polymerase (C).


Table of contents (11 chapters)

The Early Eukaryotic Fossil Record

The Diversity Of Eukaryotes And The Root Of The Eukaryotic Tree

Origin of Eukaryotic Endomembranes: A Critical Evaluation of Different Model Scenarios

Origins and Evolution of Cotranslational Transport to the ER

Evolution of the Endoplasmic Reticulum and the Golgi Complex

Mironov, Alexander A. (et al.)

An Evolutionary Perspective on Eukaryotic Membrane Trafficking

Reconstructing the Evolution of the Endocytic System: Insights from Genomics and Molecular Cell Biology

Origins and Evolution of the Actin Cytoskeleton

Origin and Evolution of Self-Consumption: Autophagy

Origin and Evolution of the Centrosome

The Evolution of Eukaryotic Cilia and Flagella as Motile and Sensory Organelles


Prokaryote Evolution: Bacteria and Archaea

Prokaryotes are mostly bacteria, and their advancements led to more complex living organisms. It has been suggested that the diverse nature of bacteria and archaebacteria resulted from this evolution. As bacteria modified structures to expand their territory and tolerance, they changed into newer species of bacteria with diverse structures and functions. Due to their uniqueness, bacteria are classified in their own kingdom!

Advancements in the structure and function of prokaryotes continued to the juncture where two separate types are now identifiable: bacteria and archaea.

Bacteria and Cyanobacteria

Bacteria are the most common and well studied because they are the easiest to find and have historically been the source of many human maladies, such as bubonic plague, tuberculosis, and cholera, and the source of much advancement such as cheese, recombinant DNA, and intestinal flora, which aids in digestion and nutrient production.

Bionote

Even today, anabaena, a typical cyanobacteria, blooms in nutrient overloaded aquatic environments to produce a telltale blue-green color. Environmentalists use anabaena blooms as an indicator of environmental quality.

Bacteria appear to be simpler than archaea because they do not possess certain advanced structures typical in archaea, such as the complex RNA polymerase, the presence of interons, and branched carbon chains in lipid membranes, as well as some internal membranes. However, they do possess a cell membrane and have definite life functions. They exist alone or in colonies, in a variety of shapes, and some can endure unfavorable conditions by forming a protective endospore around the cell, which allows the cell to remain viable and dormant until favorable conditions arrive. Bacteria and archaea do possess whiplike flagella for movement.

Cyanobacteria, also known as blue-green algae, are intriguing organisms because they contain photosynthetic capabilities and are thought to be responsible for changing the prehistoric environment to an oxygen atmosphere.

Microfossil cyanobacteria estimated to be 3.5 billion years old were discovered in Australia. Their hypothesized oxygen production likely also created the protective ozone layer.

Archaea

Archaea have structures such as tRNA nucleotide sequences and RNA polymerase that are more closely related to eukaryotes than bacteria. They have adapted complex protein, carbohydrate, and lipid molecules that allow them to live and reproduce in the harshest environments where nothing else will live. In fact, archaea are so different from bacteria that they are also classified in their own kingdom, separate from all other organisms! Many species are autotrophic and obtain energy through the chemosynthesis of carbon dioxide instead of the photosynthesis of carbon dioxide. Because of their extreme lifestyle, they do not have the history of scientific investigation that bacteria have generated, although they contain the solutions for expanding the genetic territory of other helpful microorganisms. For example, archaebacteria thrive in the hot springs in Yellowstone National Park where the water temperature is measured at 194F (90C).



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