At the same time, comparative-genomic and ultrastructural studies destroyed the biological underpinning of the near-root positions of the former early branching groups of protists by showing that none of them ancestrally lack mitochondria, as they all have genes of apparent mitochondrial origin and mitochondria-related organelles, such as hydrogenosomes and mitosomes [ 11 , 12 , 13 , 40 ].
There are therefore no grounds to consider any group of eukaryotes primitive, a presymbiotic archezoan. Rather, taking into account the small genomes and high rate of evolution characteristic of most of the protist groups thought to be early branching, and their parasitic lifestyle, it is becoming increasingly clear that most or perhaps all of them evolved from more complex ancestral forms by reductive evolution [ 37 , 39 ].
Reductive evolution refers to the evolutionary modality typical of parasites: they tend to lose genes, organelles and functions when the respective functionalities are taken over by the host. So the archezoan crown group phylogeny seems to have been disproved, and deep phylogeny and the theories of the origin of eukaryotes effectively had to start from scratch.
This time phylogenomic approaches were mainly used, that is, phylogenetic analysis of genome-wide sets of conserved genes; this was made possible by the much larger number of genomes that had been sequenced [ 41 , 42 ].
The key accomplishment at this new stage was the proposal of 'supergroups' of eukaryotes that are suggested to combine highly diverse groups of organisms in a monophyletic group [ 36 , 43 — 45 ]. Most of the phylogenomic analyses published so far converge on five supergroups or six if the Amoebozoa and Opisthokonts do not form a single supergroup, the Unikonts; Figure 1.
Although proving monophyly is non-trivial for these groups [ 46 — 48 ], the general structure of the tree, with a few supergroups forming a star-like phylogeny Figure 1 , is reproduced consistently, and the latest results [ 49 — 52 ] seem to support the monophyly of the five supergroups. Evolution of the eukaryotes. The relationship between the five eukaryotic supergroups - Excavates, Rhizaria, Unikonts, Chromalveolates and Plantae - are shown as a star phylogeny with LECA placed in the center.
The 4, genes assigned to LECA are those shared by the free-living excavate amoeboflagellate Naegleria gruberi with representatives of at least one other supergroup [ 67 ]. The numbers of these putative ancestral genes retained in selected lineages from different supergroups are also indicated. Branch lengths are arbitrary. Two putative root positions are shown: I, the Unikont-Bikont rooting [ 56 , 57 ]; II, rooting at the base of Plantae [ 60 ]. The relationship between the supergroups is a formidable problem as the internal branches are extremely short, suggesting that the radiation of the supergroups occurred rapidly on the evolutionary scale , perhaps resembling an evolutionary 'big bang' [ 53 — 55 ].
Two recent, independent phylogenetic studies [ 51 , 52 ] each analyzed over conserved proteins from several dozen eukaryotic species and, after exploring the effects of removing fast-evolving taxa, arrived at a three-megagroup structure of the eukaryotic tree. The megagroups consist of Unikonts, Excavates, and the assemblage of Plantae, Chromalveolata and Rhizaria [ 51 , 52 ].
Furthermore, there have been several attempts to infer the position of the root of the eukaryotic tree Figure 1. The first alternative to the crown group tree was proposed by Cavalier-Smith and coworkers [ 56 — 58 ], who used rare genomic changes RGCs [ 59 ], such as the fusion of two enzyme genes [ 56 , 57 ] and the domain structure of myosins [ 58 ], to place the root between the Unikonts and the rest of eukaryotes I red arrow in Figure 1.
This separation seems biologically plausible because Unikont cells have a single cilium, whereas all other eukaryotic cells have two. However, this conclusion could be suspect because the use of only a few RGCs makes it difficult to rule out homoplasy parallel emergence of the same RGC, such as gene fusion or fission, in different lineages. Rogozin and coworkers [ 60 ] used a different RGC approach based on rare replacements of highly conserved amino acid residues requiring two nucleotide substitutions and inferred the most likely position of the root to be between Plantae and the rest of eukaryotes II green arrow in Figure 1.
Again, this seems biologically plausible because the cyanobacterial endosymbiosis that gave rise to plastids occurred on the Plantae lineage.
The controversy about the root position and the lack of consensus regarding the monophyly of at least some of the supergroups, let alone the megagroups, indicate that, despite the emerging clues, the deep phylogeny of eukaryotes currently should be considered unresolved.
In a sense, given the likely 'big bang' of early eukaryote radiation, the branching order of the supergroups, in itself, might be viewed as relatively unimportant [ 61 ]. However, the biological events that triggered these early radiations are of major interest, so earnest attempts to resolve the deepest branches of the eukaryotic tree will undoubtedly continue with larger and further improved datasets and methods.
Comparative analysis of representative genomes from different eukaryotic supergroups enables the reconstruction of the gene complement of LECA using maximum parsimony MP or more sophisticated maximum likelihood ML methods [ 62 — 64 ]. Essentially, genes that are represented in diverse extant representatives of different supergroups, even though lost in some lineages, can be mapped back to LECA.
The results of all these reconstructions consistently point to a complex LECA, in terms of both the sheer number of ancestral genes and, perhaps even more importantly, the ancestral presence of the signature functional systems of the eukaryotic cell see below. A MP reconstruction based on phyletic patterns in clusters of orthologous genes of eukaryotes mapped 4, genes to LECA Figure 1 [ 63 , 65 , 66 ].
Remarkably, an even simpler estimation, based on the recent analysis of the genome of Naegleria gruberi , the first sequenced genome of a free-living excavate [ 67 ], revealed about a nearly identical number of genes, 4,, that are shared by Naegleria and at least one other supergroup of eukaryotes, suggesting that these genes are part of the LECA heritage Figure 1.
Such estimates are highly conservative as they do not account for lineage-specific loss of ancestral genes, a major aspect in the evolution of eukaryotes. Given that the current estimate for the gene complement of LECA must be conservative, the genome of LECA is likely to have been as complex as those of typical extant free-living unicellular eukaryotes [ 68 ]. This conclusion is supported by reconstructions from comparative genomics of the ancestral composition of the key functional systems of the LECA, such as the nuclear pore [ 28 , 69 ], the spliceosome [ 29 ], the RNA interference machinery [ 70 ], the proteasome and the ubiquitin signaling system [ 71 ], and the endomembrane apparatus [ 10 ].
The outcomes of these reconstructions are all straightforward and consistent, even when different topologies of the phylogenetic tree of eukaryotes were used as the scaffold for the reconstruction: LECA already possessed all these structures in its fully functional state, possibly as complex as the counterparts in modern eukaryotes.
Reconstruction of other aspects of the genomic composition and architecture of LECA similarly points to a highly complex ancestral genome. Comparative-genomic analysis of intron positions in orthologous genes within and between supergroups suggests high intron densities in the ancestors of the supergroups and in LECA, at least as dense as in modern free-living unicellular eukaryotes [ 72 — 75 ].
A systematic analysis of widespread gene duplications in eukaryotes indicates that hundreds of duplications predate LECA, especially duplications of genes involved in protein turnover [ 63 , 65 , 66 ]. Taken together, these results clearly indicate that LECA was a typical, fully developed eukaryotic cell.
The subsequent evolution of eukaryotes has seemingly shown no consistent trend toward increased complexity, except for lineage-specific embellishments, such as those seen in animals and plants.
There was obviously an important stage of evolution on the 'stem' of eukaryotes, after they first evolved but before LECA, which included extensive duplication of numerous essential genes, so that the set of ancestral genes approximately doubled [ 63 , 65 , 66 ]. Eukaryotes are hybrid organisms in terms of both their cellular organization and their gene complement. The gene complement of eukaryotes is an uneven mix of genes of apparent archaeal origin, genes of probable bacterial origin, and genes that so far seem eukaryote-specific, without convincing evidence of ancestry in either of the two prokaryote domains Figure 2.
Paradoxical as this might appear, although trees based on rRNA genes and concatenated alignments of information-processing proteins, such as polymerases or splicing proteins, both put archaea and eukaryotes together, genome-wide analyses consistently and independently show that there are three or more times more genes with bacterial homologs than with archaeal homologs [ 62 , 63 , 78 , 79 ] Figure 2.
The archaeal subset is strongly enriched in information processing functions translation, transcription, replication, splicing , whereas the bacterial subset consists largely of metabolic enzymes [ 62 , 78 ] see below for more details. Breakdown of the genes from two eukaryotes by the putative evolutionary affinities. The putative origin of genes was tentatively inferred from the best hits obtained by searching the NCBI non-redundant protein sequence database using the BLASTP program [ ], with all protein sequences from the respective organisms used as queries.
Although sequence similarity searches are often regarded as a very rough approximation of the phylogenetic position [ ], the previous analysis of the yeast genome showed a high level of congruence between the best hits and phylogenomic results [ 78 ].
Major archaeal and bacterial groups are color-coded and denoted 1 to 18; the number of proteins with the best hit to the given groups is indicated. However, attempts to pinpoint the specific archaeal and bacterial 'parents' of eukaryotes reveal complicated evolutionary relationships.
Apart from this uncertainty about the gene complement of the endosymbiont, it is impossible to rule out multiple sources of the bacterial-like genes in eukaryotes [ 83 ], which may have origins other than the genome of the bacterial endosymbiont.
In particular, whatever the actual nature of the archaeal-like ancestor, it probably lived at moderate temperatures and non-extreme conditions and was consequently in contact with a diverse bacterial community.
Modern archaea with such lifestyles have numerous genes of diverse bacterial origins, indicating extensive horizontal acquisition of genes from bacteria [ 84 , 85 ]. Thus, the archaeal-like host of the endosymbiont could have already had many bacterial genes, partly explaining the observed pattern. Phylogenomic studies using different methods point to different archaeal lineages - Crenarchaeota [ 86 , 87 ], Euryarchaeota [ 88 ], or an unidentified deep branch [ 89 , 90 ] - as the candidates for the eukaryote ancestor Figure 3.
Unequivocal resolution of such deep evolutionary relationships is extremely difficult. Moreover, at least one of these analyses [ 89 ] explicitly suggests the possibility that the archaeal heritage of eukaryotes is genuinely mixed, with the largest contribution coming from a deep lineage, followed by the contributions from Crenarchaeota Thaumoarchaeota and the Euryarchaeota Figure 3. In the next section I examine the possibility of multiple archaeal and bacterial ancestors of the eukaryotes with respect to distinct functional systems of eukaryotic cells.
Possible archaeal origins of eukaryotic genes. The archaeal tree is shown as a bifurcation of Euryarchaeota and the putative second major branch combining Crenarchaeota, Thaumarchaeota, and Korarchaeota [ ]; deep, possibly extinct lineages are shown as a single stem. Some of the most compelling indications on the course of evolution and the nature of ancestral forms come from signature genes that are uniquely shared by two or more major lineages and from detailed evolutionary analysis of well characterized functional systems, in particular the signature systems of the eukaryotic cell.
Comparative genome sequence analysis has revealed that some of the key molecular machines of the eukaryotes, and not only those directly involved in information processing, can be confidently derived from archaeal ancestors Table 1 and Figure 4. Strikingly, this archaeal heritage seems to be patchy with respect to the specific origins, with apparent evolutionary affinities to different groups of archaea Table 1 and Figure 4.
For instance, comparative analysis of the translation system components tends to suggest an affinity between eukaryotes and Crenarchaeota [ 91 ]. Similarly, the core transcription machinery of eukaryotes shares some important proteins with Crenarchaeota, Thaumarchaeota and Korarchaeota, to the exclusion of Euryarchaeota [ 92 — 94 ]. By contrast, the histones, the primary components of nucleosomes, are missing in most of the Crenarchaeota but invariably conserved in Euryarchaeota and also present in Korarchaeum and some Thaumarchaeota [ 95 ].
Apparent complex origins of some key functional systems of eukaryotes. The domains are not drawn to scale. Eukaryotic cell division components are also conserved in several but not all of the major archaeal lineages. For example, homologs of the ESCRT-III complex, which performs key roles in vesicle biogenesis and cytokinesis in eukaryotes, are responsible for cell division in the Crenarchaeota but are missing in most of the Euryarchaeota, which possess a bacterial-like division mechanism using the GTPase FtsZ, a distant homolog of tubulin [ 96 , 97 ].
Eukaryote B-family DNA polymerases, a group of four paralogs that are collectively responsible for genome replication, show a complex pattern of ancestry Figure 4 : one branch of the eukaryotic polymerases seems to have evolved from archaeal PolBI, which is conserved in all archaea, whereas the other branch appears to derive from the Crenarchaea-specific PolBII [ 99 , ].
Another major theme emerging from these studies is the bacterial contribution and the formation of archaeao-bacterial chimeras Table 1 and Figure 4. A clear-cut case of a chimeric eukaryotic system is the RNA interference machinery, in which one of the key proteins, the endonuclease Dicer, consists of two bacterial RNAse III domains and a helicase domain of apparent euryarchaeal origin, and the other essential protein, Argonaute, also shows a euryarchaeal affinity Figure 4 [ 70 , ].
The nuclear pore complex, a quintessential eukaryotic molecular machine, does not show any indications of archaeal ancestry but rather consists of proteins of apparent bacterial origin combined with proteins consisting of simple repeats whose provenance is difficult to ascertain [ 28 ]. These observations suggest that the archaeal ancestor of eukaryotes combined a variety of features found separately in diverse extant archaea.
This inference is consistent with the results of phylogenomic analysis and evolutionary reconstruction discussed above. Thus, the currently existing archaeal lineages probably evolved by differential streamlining, or reductive evolution of the complex ancestral forms, whereas eukaryotes largely retained the ancestral complexity.
The diverse origins of eukaryotic functional systems has major implications for how eukaryotes originated, as explained below. The results of comparative genomics and ultrastructural studies do not yet definitively show where the eukaryotic cell came from, but they do offer important insights. Box 1 lists the key observations that must be included in any evolutionary scenario for the evolution of eukaryotes called eukaryogenesis and summarizes the two alternative scenarios, which are depicted in Figure 5.
The main issue revolves around the role of endosymbiosis [ 2 , 3 , , ]: was it the cause of the entire chain of events that led to the emergence of LECA the stem phase of evolution , as proposed by the symbiogenesis scenario, or was it a step in the evolution of the already formed eukaryotic cell, as proposed by the archaezoan scenario?
The two alternative scenarios of eukaryogenesis. Given that eukaryogenesis may have been a unique event and that intermediate stages in the process cannot be seen, these questions are enormously difficult, and final answers might not be attainable.
But the symbiogenesis scenario seems to be more plausible than the archaezoan scenario [ ], for three main reasons. First, under the archaezoan scenario, there is no plausible selective force behind the evolution of the nucleus, and in particular the elaborate nuclear pore complex. The nucleus disrupts the transcription-translation coupling that is typical of bacteria and archaea [ — ] and necessitates the evolution of the time- and energy-consuming mechanism of nucleocytosolic transport of mRNA.
At least some additional innovations of eukaryogenesis, such as the evolution of the nonsense-mediated decay of transcripts containing premature stop codons and expansion of the ubiquitin system, can be envisaged as part of the same chain of adaptations to the intron bombardment as the origin of the nucleus [ ] Figure 5.
However, some species form filaments or colonies of the same species. They move around as they have locomotory organs, such as pseudopods, cilia, and flagella. Others lack these organs and therefore are non-motile. Protists include the following: 1 protozoa, the animal-like protists, 2 algae, the plant-like protists, and 3 slime molds and water molds, the fungus-like protists. Life, as we know it today, is presumed to have started in the sea and many of them were likely eukaryotic animal-like organisms.
Because of the expanding diversity of animal life forms, taxonomists eventually came up with a classification scheme to group them into various phyla. Know more about the early animals that were likely the first ones to roam the ancient seas through this tutorial Read More.
It only takes one biological cell to create an organism. A single cell is able to keep itself functional through its 'miniature machines' known as organelles.
Read this tutorial to become familiar with the different cell structures and their functions Skip to content Main Navigation Search. Dictionary Articles Tutorials Biology Forum. Table of Contents. Quiz Choose the best answer. What is a eukaryote? A single-celled organism. An organism that has a nucleus.
An organism that lacks membrane-bound organelles. Which of these organisms are eukaryotes? Membrane-bound structures inside a cell Organelles. Unicellular eukaryotes Archaea. Multicellular eukaryotes Animals. Your Name. To Email. Time is Up! Primitive Animals Life, as we know it today, is presumed to have started in the sea and many of them were likely eukaryotic animal-like organisms.
Biological Cell Introduction It only takes one biological cell to create an organism. Related Articles ATP represents the short-term stored energy of the cell. Cellular respiration is the process of making ATP using the chemical energy found in glucose and other nutrients. In mitochondria, this process uses oxygen and produces carbon dioxide as a waste product.
In fact, the carbon dioxide that you exhale with every breath comes from the cellular reactions that produce carbon dioxide as a by-product. It is important to point out that muscle cells have a very high concentration of mitochondria that produce ATP. Your muscle cells need a lot of energy to keep your body moving.
Instead, the small amount of ATP they make in the absence of oxygen is accompanied by the production of lactic acid. In addition to the aerobic generation of ATP, mitochondria have several other metabolic functions. One of these functions is to generate clusters of iron and sulfur that are important cofactors of many enzymes. Such functions are often associated with the reduced mitochondrion-derived organelles of anaerobic eukaryotes.
There are two hypotheses about the origin of mitochondria: endosymbiotic and autogenous, but the most accredited theory at present is endosymbiosis. The endosymbiotic hypothesis suggests mitochondria were originally prokaryotic cells, capable of implementing oxidative mechanisms.
These prokaryotic cells may have been engulfed by a eukaryote and became endosymbionts living inside the eukaryote. Although they are both eukaryotic cells, there are unique structural differences between animal and plant cells. Each eukaryotic cell has a plasma membrane, cytoplasm, a nucleus, ribosomes, mitochondria, peroxisomes, and in some, vacuoles; however, there are some striking differences between animal and plant cells.
While both animal and plant cells have microtubule organizing centers MTOCs , animal cells also have centrioles associated with the MTOC: a complex called the centrosome. Animal cells each have a centrosome and lysosomes, whereas plant cells do not. Plant cells have a cell wall, chloroplasts and other specialized plastids, and a large central vacuole, whereas animal cells do not.
The centrosome is a microtubule-organizing center found near the nuclei of animal cells. It contains a pair of centrioles, two structures that lie perpendicular to each other. Each centriole is a cylinder of nine triplets of microtubules. The centrosome the organelle where all microtubules originate replicates itself before a cell divides, and the centrioles appear to have some role in pulling the duplicated chromosomes to opposite ends of the dividing cell.
The Centrosome Structure : The centrosome consists of two centrioles that lie at right angles to each other. Each centriole is a cylinder made up of nine triplets of microtubules. Nontubulin proteins indicated by the green lines hold the microtubule triplets together. Animal cells have another set of organelles not found in plant cells: lysosomes.
Enzymes within the lysosomes aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. These enzymes are active at a much lower pH than that of the cytoplasm. Therefore, the pH within lysosomes is more acidic than the pH of the cytoplasm. Many reactions that take place in the cytoplasm could not occur at a low pH, so the advantage of compartmentalizing the eukaryotic cell into organelles is apparent. The cell wall is a rigid covering that protects the cell, provides structural support, and gives shape to the cell.
Fungal and protistan cells also have cell walls. While the chief component of prokaryotic cell walls is peptidoglycan, the major organic molecule in the plant cell wall is cellulose, a polysaccharide comprised of glucose units. When you bite into a raw vegetable, like celery, it crunches. The dashed lines at each end of the figure indicate a series of many more glucose units. The size of the page makes it impossible to portray an entire cellulose molecule.
Like mitochondria, chloroplasts have their own DNA and ribosomes, but chloroplasts have an entirely different function. Chloroplasts are plant cell organelles that carry out photosynthesis.
Photosynthesis is the series of reactions that use carbon dioxide, water, and light energy to make glucose and oxygen. This is a major difference between plants and animals; plants autotrophs are able to make their own food, like sugars, while animals heterotrophs must ingest their food.
The fluid enclosed by the inner membrane that surrounds the grana is called the stroma. The Chloroplast Structure : The chloroplast has an outer membrane, an inner membrane, and membrane structures called thylakoids that are stacked into grana. The space inside the thylakoid membranes is called the thylakoid space. The light harvesting reactions take place in the thylakoid membranes, and the synthesis of sugar takes place in the fluid inside the inner membrane, which is called the stroma.
The chloroplasts contain a green pigment called chlorophyll, which captures the light energy that drives the reactions of photosynthesis. Like plant cells, photosynthetic protists also have chloroplasts. Some bacteria perform photosynthesis, but their chlorophyll is not relegated to an organelle. When you forget to water a plant for a few days, it wilts. As the central vacuole shrinks, it leaves the cell wall unsupported. This loss of support to the cell walls of plant cells results in the wilted appearance of the plant.
The central vacuole also supports the expansion of the cell. When the central vacuole holds more water, the cell gets larger without having to invest a lot of energy in synthesizing new cytoplasm.
Privacy Policy. Skip to main content. Cell Structure. Search for:. Eukaryotic Cells. Characteristics of Eukaryotic Cells A eukaryotic cell has a true membrane-bound nucleus and has other membranous organelles that allow for compartmentalization of functions. Learning Objectives Describe the structure of eukaryotic cells. Mitochondria are responsible for ATP production; the endoplasmic reticulum modifies proteins and synthesizes lipids; and the golgi apparatus is where the sorting of lipids and proteins takes place.
Peroxisomes carry out oxidation reactions that break down fatty acids and amino acids and detoxify poisons; vesicles and vacuoles function in storage and transport.
Animal cells have a centrosome and lysosomes while plant cells do not. Plant cells have a cell wall, a large central vacuole, chloroplasts, and other specialized plastids, whereas animal cells do not. Key Terms eukaryotic : Having complex cells in which the genetic material is organized into membrane-bound nuclei.
The Plasma Membrane and the Cytoplasm The plasma membrane is made up of a phospholipid bilayer that regulates the concentration of substances that can permeate a cell.
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