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Defending the Christian Worlview, Creationism, and Intelligent Design » Molecular biology of the cell » Eukaryotic cells, and their origin

Eukaryotic cells, and their origin

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1Eukaryotic cells, and their origin Empty Eukaryotic cells, and their origin Fri Dec 20, 2013 1:17 pm


Origin of eukaryotes

Eukaryotic cells, and their origin Eukary10

Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?  1

On average, the volume of eukaryotic cells is about 15,000 times larger than that of prokaryotic cells. 4 The origin of eukaryotes is a fundamental, forbidding evolutionary puzzle. Comparative genomic analysis clearly shows that the last eukaryotic common ancestor (LECA) possessed most of the signature complex features of modern eukaryotic cells, in particular the mitochondria, the endomembrane system including the nucleus, an advanced cytoskeleton and the ubiquitin network. Numerous duplications of ancestral genes, e.g. DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. Thus, the LECA was not a primitive organism and its emergence must have resulted from extensive evolution towards cellular complexity. However, the scenario of eukaryogenesis, and in particular the relationship between endosymbiosis and the origin of eukaryotes, is far from being clear. Four recent developments provide new clues to the likely routes of eukaryogenesis. First, evolutionary reconstructions suggest complex ancestors for most of the major groups of archaea, with the subsequent evolution dominated by gene loss. Second, homologues of signature eukaryotic proteins, such as actin and tubulin that form the core of the cytoskeleton or the ubiquitin system, have been detected in diverse archaea. The discovery of this ‘dispersed eukaryome’ implies that the archaeal ancestor of eukaryotes was a complex cell that might have been capable of a primitive form of phagocytosis and thus conducive to endosymbiont capture. Third, phylogenomic analyses converge on the origin of most eukaryotic genes of archaeal descent from within the archaeal evolutionary tree, specifically, the TACK superphylum. Fourth, evidence has been presented that the origin of the major archaeal phyla involved massive acquisition of bacterial genes. Taken together, these findings make the symbiogenetic scenario for the origin of eukaryotes considerably more plausible and the origin of the organizational complexity of eukaryotic cells more readily explainable than they appeared until recently.

The origin of eukaryotes is one of the hardest and most intriguing problems in the study of the evolution of life, and arguably, in the whole of biology. Compared to archaea and bacteria (collectively, prokaryotes), eukaryotic cells are three to four orders of magnitude larger in volume and display a qualitatively higher level of complexity of intracellular organization. Unlike the great majority of prokaryotes, eukaryotic cells possess an extended system of intracellular membranes that includes the eponymous eukaryotic organelle, the nucleus, and fully compartmentalizes the intracellular space. In eukaryotic cells, proteins, nucleic acids and small molecules are distributed by specific trafficking mechanismsrather than by free diffusion as is largely the case in bacteria and archaea. Thus, eukaryotic cells function on different physical principles compared to prokaryotic cells, which is directly due to their (comparatively) enormous size. The gulf between the cellular organizations of eukaryotes and prokaryotes is all the more striking because no intermediates have been found. Comparative analysis of eukaryotic cells and genomes confidently maps highly advanced functional systems and macromolecular complexes to the last eukaryotic common ancestor (LECA). The actin and tubulin cytoskeletons, the nuclear pore, the spliceosome, the proteasome and the ubiquitin signalling system are only a few of the striking examples of the organizational complexity that seems to be a ‘birthright’ of eukaryotic cells. The formidable problem that these fundamental complex features present to evolutionary biologists makes Darwin’s famous account of the evolution of the eye look like a simple, straightforward case. Indeed, so intimidating is the challenge of eukaryogenesis that the infamous notion of irreducible complexity’ has sneaked into serious scientific debate 2.

Molecular phylogenetics and phylogenomics revealed fundamental aspects of the origin of eukaryotes. The ‘standard model’ of molecular evolution, derived primarily from the classic phylogenetic analysis of 16S RNA by Woese and co-workers and supported by subsequent phylogenetic analyses of universal genes, identifies eukaryotes as the sister group of archaea, to the exclusion of bacteria. Within the eukaryotic part of the tree, early phylogenetic studies have placed into the root position several groups of unicellular organisms, primarily parasites, that unlike the majority of eukaryotes, lack mitochondria. These organisms have been construed as ‘archezoa’, i.e. the primary amitochondrial eukaryotes that were thought to have hosted the proto-mitochondrial endosymbiont

Eukaryotic cells, and their origin IK1I0jP

However, advances of comparative genomics jointly with discoveries of cell biology have put the archezoan scenario of eukaryogenesis into serious doubt. First, it has been shown that all the purported archezoa possess organelles, such as  hydrogenosomes and mitosomes, that appeared to be derivatives of the mitochondria. These mitochondria-like organelles typically lack genomes but contain proteins encoded by genes of apparent bacterial origin that encode homologous mitochondrial proteins in other eukaryotes. Combined, the structural and phylogenetic observations leave no reasonable doubt that hydrogenosomes and mitosomes indeed evolved from the mitochondria. Accordingly, no primary amitochondrial eukaryotes are currently known, suggesting that the primary a-proteobacterial endosymbiosis antedated the LECA. Compatible with this conclusion, subsequent, refined phylogenetic studies have placed the former ‘archezoa’ within different groups of eukaryotes indicating that their initial position at the root was an artefact caused by their fast evolution, most probably causally linked to the parasitic lifestyle . These parallel developments left the archezoan scenario without concrete support but have not altogether eliminated its attractiveness. An adjustment to the archezoan scenario simply posited that the archezoa was an extinct group that had been driven out of existence by the more efficient mitochondrial eukaryotes. A concept predicated on an extinct group of organisms that is unlikely to have left behind any fossils and is refractory to evolutionary reconstruction due to the presence of mitochondria (or vestiges thereof ) in all eukaryotes is quite difficult to refute but can hardly get much traction without any concrete evidence of the existence of archezoa.

A major problem faced by this scenario (and symbiogenetic scenarios in general) is the mechanistic difficulty of the engulfment of one prokaryotic cell by another. Comparative analysis of the increasingly diverse collection of archaeal and bacterial genomes has yielded multiple lines of evidence that might change the notion of the implausibility of an archaeo-bacterial endosymbiosis.

The diversity of the outcomes of phylogenetic analysis, with the origin of eukaryotes scattered around the archaeal diversity, has led to considerable frustration and suggested that a ‘phylogenomic impasse’ has been reached, owing to the inadequacy of the available phylogenetic methods for disambiguating deep relationships

In the context of the classical view of the universal tree of life, the Archaea and the Eukarya have a common ancestor, the nature of which remains undetermined.The contradiction is evident.  

The reconstructions suggest that the genome of the LECA was at least as complex as those of typical extant free-living unicellular eukaryotes (Koonin, 2010a).


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Evolution by Reduction? (Science Highlights) 2

The origins of eukaryotes remain controversial and somewhat enigmatic. Kurland et al. (p. 1011) provide a counterpoint to current models in which the eukaryotic cell is derived from structurally and genetically less complex prokaryotic cells. On the basis of genomic and proteomic evidence, they suggest that the essence of eukaryotic cellular complexity existed in the common ancestor of eucarya, bacteria, and archaea, and that the bacteria and archaea have evolved by genome reduction driven by specialization for fast growth and cell division and/or adaptation to extreme environments.

Genomics and the Irreducible Nature of Eukaryote Cells 1)

Large-scale comparative genomics in harness with proteomics has substantiated fundamental features of eukaryote cellular evolution. The evolutionary trajectory of modern eukaryotes is  distinct from that of prokaryotes. Data from many sources give no direct evidence that eukaryotes evolved by genome fusion between archaea and bacteria. Comparative genomics shows that, under  certain ecological settings, sequence loss and cellular simplification are common modes of  evolution. Subcellular architecture of eukaryote cells is in part a physical-chemical consequence of molecular crowding; subcellular compartmentation with specialized proteomes is required for the efficient functioning of proteins.

Comparative genomics and proteomics have strengthened the view that modern  eukaryote and prokaryote cells have long followed separate evolutionary trajectories. Because their cells appear simpler, prokaryotes have traditionally been considered ancestors of eukaryotes. Nevertheless, comparative genomics has confirmed a lesson from paleontology: Evolution does not proceed monotonically from the simpler to the more complex . Here, we review recent data from proteomics and genome sequences suggesting that eukaryotes are a unique primordial lineage. Mitochondria, mitosomes, and hydrogenosomes are a related family of organelles that distinguish eukaryotes from all prokaryotes. Recent analyses also suggest that early eukaryotes had many introns, and RNAs and proteins found in modern spliceosomes. Indeed, it seems that life-history parameters affect intron numbers. In addition, Bmolecular crowding is now recognized as an  important physical-chemical factor contributing  to the compartmentation of even the earliest eukaryote cells. Nuclei, nucleoli, Golgi apparatus, centrioles, and endoplasmic reticulum are examples of cellular signature structures (CSSs) that distinguish eukaryote cells from archaea and bacteria. Comparative genomics, aided by proteomics of CSSs such as the mitochondria , nucleoli, and spliceosomes, reveals hundreds of proteins with no orthologs evident in the genomes of prokaryotes; these are the eukaryotic signature proteins (ESPs). The many ESPs within the subcellular structures of eukaryote cells provide landmarks to track the trajectory of eukaryote genomes from their origins. In contrast, genome fusion between archaea and bacteria are surprisingly uninformative about the emergence of the cellular and genomic signatures of eukaryotes (CSSs and ESPs). The failure of genome fusion to directly explain any characteristic feature of the eukaryote cell is a critical starting point for studying eukaryote

Eukaryotic cells, and their origin Common10

It is agreed that, whether using gene content, protein-fold families, or RNA sequences, the unrooted tree of life divides into archaea, bacteria, and eukaryotes (Fig. 1). On such unrooted trees, the three domains diverge   from a population that can be called the last universal common ancestor (LUCA). However, LUCA  means different things to different people, so we prefer to call it a common ancestor; in this case it is the hypothetical feeding mode in an ancestor of eukaryotes. This uniquely eukaryote feeding mode requires a larger and more complex cell, consistent with earlier suggestions that a unicellular raptor (predator), which acquired a bacterial endosymbiont/mitochondria lineage, became the common ancestor of all modern eukaryotes . Indeed, predator/prey relationships may provide the ecological setting for the divergence of the distinctive cell types adopted by eukaryotes, bacteria, and archaea.

Proteomics of Cell Compartments

Comparative genomics and proteomics reveal phylogenetic relationships between proteins making up eukaryote subcellular features and those found in prokaryotes. We distinguish three main phylogenetic classes; the first are proteins that are unique to eukaryotes: the ESPs. The ESPs we place in three subclasses: proteins arising de novo in eukaryotes; proteins so divergent to homologs of other domains that their relationship is largely lost; or finally, descendants of proteins that are lost from other domains, surviving only as ESPs in eukaryotes.  The second class contains interdomain horizontal gene transfers; these are proteins occurring in two domains with the lineage of one domain rooted within their homologs in a second domain. The third class contains homologs found in at least two domains, but the proteins of one domain are not rooted within another domain(s); instead, the homologs appear to descend from the common ancestor (Fig. 1). Most eukaryote proteins shared by prokaryotes are distant, rather than close, relatives. Thus, proteins shared between domains appear to be descendants of the common ancestor; few seem to result from interdomain

Although the genomes of mitochondria are clearly descendants of a-proteobacteria, proteomics and comparative genomics identify relatively few proteins in yeast and human lateral gene transfer mitochondria descended from the ancestral ubiquitins, and some GTP binding proteins are tween 20 and 30% of weight or volume. bacterium. Several hundred among the most highly conserved eukaryotic. Such densities are described as ''molecular genes have been transferred from the ancestral proteins. These may be descendants of the com- crowding'' because the space between macro- bacterium to the nuclear genome, but most mon ancestor recruited early in the evolution of molecules is much less than their diameters;

mitochondria descended from the ancestral bacterium. Several hundred genes have been transferred from the ancestral bacterium to the nuclear genome, but most proteins from the original endosymbiont have been lost. For yeast, the largest protein class contains more than 200 eukaryote proteins (ESPs) targeted to the mitochondrion but encoded in the nucleus. In addition, the yeast nucleus encodes 150 mitochondrial proteins not uniquely identifiable with a single domain but apparently eukaryotic descendants from the common ancestor. Accordingly, the yeast and human mitochondria proteomes emerge largely as products of the eukaryotic nuclear genome (85%) and only to a lesser degree (15%) as direct descendants of endosymbionts. The strong representation of ESPs in their proteomes means that mitochondria and their descendants are usefully viewed as ‘‘honorary’’ CSSs. There are substantial numbers of ESPs in the other CSSs. For the proteome of the reduced anaerobic parasite Giardia lamblia, searches of 2136 proteins found in each of Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, and Arabidopsis thaliana yielded 347 ESPs for G. lamblia. This was reduced to roughly 300 by rigorous screening, with ESPs distributed between nuclear and cytoplasmic compartments
(Fig. 2) .

Eukaryotic cells, and their origin Distri10

The ubiquity of the ESPs and the absence of archaeal descendants are not easily explained by a prokaryote genome fusion model. The simplest interpretation is that the host for the endosymbiont/ mitochondrial lineage was an ancestral eukaryote. Similar results are obtained for another reduced eukaryote, the intracellular parasite Encephalitozoon cuniculi. A recent study identified 401 ESPs, of which 295 had homologs among the ESPs of G. lamblia.Two major categories of ESPs in the G. lamblia and E. cuniculi genomes were distinguished: those associated with the CSSs (Fig. 2) and those involved in control functions such as guanosine triphosphate (GTP) binding proteins, kinases, and phosphatases. It was also observed that many characteristic eukaryotic proteins with weak sequence homology to prokaryotic proteins but more convincing homologies of structural fold such as the actins, tubulins, kinesins, ubiquitins, and some GTP binding proteins are among the most highly conserved eukaryotic proteins. These may be descendants of the common ancestor recruited early in the evolution of the eukaryotic nuclear genome. Nucleolar proteomes are examples of essential eukaryote compartments not wrapped in double membranes and where there is no suspicion of an endosymbiotic origin. From 271 proteins in the human nucleolar proteome, 206 protein folds were identified and classified phylogenetically. Of these, 109 are eukaryotic signature folds, and the remaining ones appear to be descendants of the common ancestor, occurring in two or three domains. The spliceosome is a unique molecular machine that removes introns from eukaryote mRNAs. Even though we do not know the ancestral processing signals for the earliest eukaryotes, roughly half of the 78 spliceosomal proteins likely to be present in the ancestral spliceosome are ESPs, whereas the other half containing the Sm/LSm proteins have homologs in bacteria and archaea. These distributions of both ESPs as well as of putative descendants of the common ancestor suggest that many components of modern spliceosomes were present in the common ancestor. The subdivision into subcellular compartments (CSSs) with characteristic proteomes restricts proteins to volumes considerably smaller than the whole cell. Concentrations of macromolecules in cells are very high, typically between 20 and 30% of weight or volume. Such densities are described as ‘‘molecular crowding’’ because the space between macromolecules is much less than their diameters; consequently, diffusion of proteins in cells is retarded. Molecular crowding favors macromolecular associations, large complexes, and networks of proteins that support biological functions. High densities enhance the association kinetics of small molecules with proteins because the excluded volumes of the proteins reduce the effective volume through which small molecules diffuse. The sum of these effects is that the high macromolecular densities within CSSs enhance the kinetic efficiencies of proteins. The same principles apply to the smaller prokaryotic cells, but the effects are accentuated in larger cells. Subdividing high densities of proteins into more or less distinct compartments containing functionally interactive macromolecules is expected to be an early feature of the eukaryote lineage. The distinctive proteome of nucleoli demonstrates that compartmentation does not require an enclosing membrane. Furthermore, cell fusion is not required to account for, nor does it explain , the large number of eukaryote cell compartments.

Selection Gives and Selection Takes

Genomes evolve continuously through the interplay of unceasing mutation, unremitting competition, and ever-changing environments. Both sequence loss and sequence gain can result. In general, expanded genome size, along with augmented gene expression, increases the costs of cell propagation so the evolution of larger genomes and larger cells requires gains in fitness that compensate. Conversely, genome reduction is expected to lower the costs of propagation. There is an ever-present potential to improve the efficiency of cell propagation by reductive evolution. Environmental shifts may neutralize sequences, leaving no selective pressure to maintain them against the persistent flux of deleterious mutations. Such neutralized sequences eventually and inevitably disappear because of ‘‘mutational meltdown’’. Genome reduction can be achieved through differential loss of coding and noncoding sequences (compaction). Theileria has evolved through gene loss as well as compaction of its intergenic spaces, whereas Paramecium has eliminated only a small length of genes but markedly reduced the number of its introns . The complex genomes of some vertebrates (pufferfish, Takifugu) are so highly compacted that their genome lengths are reduced to one-eighth that of other vertebrates . Extreme cellular simplification is observed among anaerobic protists, including simplification of CSSs such as mitochondria and the Golgi apparatus. S.cerevisiae, which underwent a whole-genome  duplication, subsequently purged È85% of the duplicated sequences. The evolution of genome content is clearly not monotonic(Fig. 3)

Eukaryotic cells, and their origin Genome10

Genome sizes on the branches of a phylogenetic tree of fungi show irregular genome enlargement (including duplication) and reduction.  Examples of ecological circumstances driving genome reduction are seen in many intracellular endosymbionts and parasites, which gain few genes but lose many genes responsible formetabolic flexibility The mitochondrion is even more extreme in its reductive evolution; its ancestral bacterial genome has been reduced to a vestigial microgenome supported by a predominantly eukaryote proteome. Genomes of modern mitochondria encode between 3 and 67 proteins, whereas the smallest known free-living a-proteobacterium (Bartonella quintana) encodes È1100 proteins. Taking Bartonella as a minimal genome for the freeliving ancestor of mitochondria, nearly all of the bacterial coding sequences have been lost from the organelle, though not necessarily from the eukaryote cell. The mitochondrial genome of the protist Reclinomonas americana is the largest known but has still lost more than 95% of its original coding capacity. This abbreviated account of genome reduction illustrates the Darwinian view of evolution as a reversible process in the sense that ‘‘eyes can be acquired and eyes can be lost.’’ Genome evolution is a two-way street. This bidirectional sense of reversibility is important as an alternative to the view of evolution as a rigidly monotonic progression from simple to more complex states, a view with roots in the 18th-century theory of orthogenesis. Unfortunately, such a model has been tacitly favored by molecular biologists who appeared to view evolution as an irreversible march from simple prokaryotes to complex eukaryotes, from unicellular to multicellular. The many welldocumented instances of genome reduction provide a necessary corrective measure to the often-unstated assumption that eukaryotes must have originated from prokaryotes. 

The Hunt for the Phagotrophic Unicellular Raptor 

Proteomics, together with comparative genomics, allows glimpses of the cell structure of eukaryote ancestors. They are likely to have had introns as well as the complex machinery for removing them, and much of that RNA processing machinery still exists in their descendants. Because of molecular crowding, it is expected that interacting proteins would tend to accumulate in functional domains, making rudimentary CSSs early features of the large-celled eukaryotes. We cannot say whether there was a substantial period of time after the emergence of cells when there were no unicellular raptors or predators—a Garden of Eden. However, the identification among prokaryotes of orthologs with structural affinities to actins, tubulins, kinesins, and ubiquitins is consistent with some early organisms having evolved a phagotrophic life-style. This echoes a recurrent theme in which it was supposed that the earliest eukaryotes could feed as unicellular ‘‘raptors.’’ 

We expect that the earliest organisms were primarily auxotrophs, heterotrophs, and saprotrophs—an excellent community to support raptors. Phagotrophy is a hallmark of eukaryotic cells and is unknown among modern prokaryotes, and so it is natural to reconsider this feeding mode as a defining feature of ancestral eukaryotes. Cavalier-Smith  suggested that the ancestors of eukaryotes were phagotrophic, anaerobic free-living protists, called archeozoa. He also identified presentday anaerobic parasites such as Entamoeba, Giardia, and Microsporidia as archeozoa. However, these organisms are descendants of aerobic, mitochondriate eukaryotes . Genome reduction and cellular simplification are hallmarks of parasites and symbionts. Indeed, most of the eukaryotic anaerobes studied so far are parasites or symbionts of multicellular creatures. For the reasons outlined above, we favor the idea  that the host that acquired the mitochondrial endosymbiont was a unicellular eukaryote predator, a raptor. The emergence of unicellular raptors would have had a major ecological impact on the evolution of the gentler descendants of the common ancestor. These may have responded with several adaptive strategies: They might outproduce the raptors by rapid growth or hide from raptors by adapting to extreme environments. Thus, the hypothetical eukaryote raptors may have driven the evolution of their autotrophic, heterotrophic, and saprotrophic cousins in a reductive mode that put a premium on the relatively fast-growing, streamlined cell types we call prokaryotes.

Concluding Remarks

Genomics and proteomics have greatly increased our awareness of the uniqueness of eukaryote cells. This, together with increased understanding of molecular crowding, as well as the dynamic, often reductive nature of genome evolution, offers a new view of the origin of eukaryote cells. The eukaryotic CSSs define a unique cell type that cannot be deconstructed into features inherited directly from archaea and bacteria. Only a small fraction (È15%) of a-proteobacterial proteins are identified in the yeast and human mitochondrial proteomes; none seem to be direct descendants of archaea, and roughly half seem to be exclusively eukaryotic. The identification of the aproteobacterial descendants in this proteome validates the phylogenetic distinction between direct descent from genes transferred to the host from the bacterial endosymbiont, as opposed to descent from a hypothetical common ancestor. ESPs are important markers of the novel evolutionary trajectory of modern eukaryotes. In contrast, most proteins occur in more than one domain, and most of these could derive from the common ancestor. We take the relative abundance of signature proteins among eukaryotes to indicate that their genomes typically have a greater coding capacity than those of prokaryotes. It remains to be seen which ESPs have been lost from prokaryotes and which have been acquired by eukaryotes during their evolution. The hypothetical fusion of an archaeon and a bacterium explains nothing about the special features of the modern eukaryote cell (49), nor the many signature proteins. Nothing in global phylogenies based on ribosomal RNA, pooled proteins, and protein-fold families indicates that genome fusion generated the eukaryote lineage. Perhaps interest in fusion models arose because BLAST searches suggest that different eukaryotic coding sequences are sometimes more closely related to archaeal homologs and other times more closely related to bacterial homologs. These weak domain-specific affinities do need to be understood and alternative explanations found. However, in our view, they do not indicate that the eukaryote genome arose as a mosaic pieced together from archaeal and bacterial genomes. It is an attractively simple idea that a primitive eukaryote took up the endosymbiont/ mitochondrion by phagocytosis. A unicellular raptor with a larger, more complex cell structure than that of present-day prokaryotes is envisioned as the host of the ancestral endosymbiont. This scenario, which is not contradicted by new data derived from comparative genomics and proteomics, is a suitable starting point for future work. Acquisition of genome sequences from free-living eukaryotes among basal lineages is a high priority.

If we start with something very complex in all three cell lines, we have to suppose at least three massive chemical evolutionary events instead of only one.How far can we stretch our imaginations before we get to breaking point? ID the future!

Making the conceptual step that prokaryotes cleaved off from eukaryotes is a big step towards accepting the possibility of front loading. This is because it acknowledges that more complex preceded less complex and that’s what front loading is all about. All the empirical evidence falls neatly into place when a LUCA with a complex genome is hypothesized. Nothing makes sense in evolution except in light of a LUCA with a complex genome preprogrammed to diversify into all we see today.

1) Kurland CG, Collins LJ, Penny D. 2006 Genomics and the irreducible nature of eukaryote cells. Science 312, 1011– 1014. (doi:10.1126/science. 1121674)

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3Eukaryotic cells, and their origin Empty Re: Eukaryotic cells, and their origin Sun Oct 04, 2015 11:29 am


“Although we have written of the origin of the eukaryotes as one of the ‘major transitions,’ it was in fact a series of events: the loss of the rigid cell wall, and the acquisition of a new way of feeding on solid particles; the origin of an internal cytoskeleton, and of new methods of cell locomotion; the appearance of a new system of internal cell membranes, including the nuclear membrane; the spatial separation of transcription and translation; the evolution of rod-shaped chromosomes with multiple origins of replication, removing the limitation on genome size; and , finally, the origin of cell organelles, in particular the mitochondrion and, in algae and plants, the plastid. Of these events, at least the last two qualify as major transitions in the sense of being major changes in the way genetic information is stored and transmitted.”

Smith, John Maynard, and Eörs Szathmary. The Origins of Life. Oxford University Press. 1999. Quoted Morowitz, Harold. The Emergence of Everything. Oxford University Press. 2002. Pps. 91-2.

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Eukaryotic evolution, changes and challenges

New findings have profoundly changed the ways in which we view early eukaryotic evolution, the composition of major groups, and the relationships among them. The changes have been driven by a flood of sequence data combined with improved—but by no means consummate—computational methods of phylogenetic inference. Various lineages of oxygen-shunning or parasitic eukaryotes were once thought to lack mitochondria and to have diverged before the mitochondrial endosymbiotic event. Such key lineages, which are salient to traditional concepts about eukaryote evolution, include the diplomonads (for example, Giardia), trichomonads (for example, Trichomonas) and microsporidia (for example, Vairimorpha). From today’s perspective, many key groups have been regrouped in unexpected ways, and aerobic and anaerobic eukaryotes intermingle throughout the unfolding tree. Mitochondria in previously unknown biochemical manifestations seem to be universal among eukaryotes, modifying our views about the nature of the earliest eukaryotic cells and testifying to the importance of endosymbiosis in eukaryotic evolution. These advances have freed the field to consider new hypotheses for eukaryogenesis and to weigh these, and earlier theories, against the molecular record preserved in genomes. Newer findings even call into question the very notion of a ‘tree’ as an adequate metaphor to describe the relationships among genomes. Placing eukaryotic evolution within a time frame and ancient ecological context is still problematic owing to the vagaries of themolecular clock and the paucity of Proterozoic fossil eukaryotes that can be clearly assigned to contemporary groups. Although the broader contours of the eukaryote phylogenetic tree are emerging from genomic studies, the details of its deepest branches, and its root, remain uncertain.

5Eukaryotic cells, and their origin Empty The Origin of the Eukaryotic Cell Sun Oct 18, 2015 2:10 pm


The Origin of the Eukaryotic Cell1

Although bacteria can sometimes be as large as a typical eukaryotic cell and can harbor as many as10,000 genes (66), spectacular individual complexity is a feature of the eukaryotes. Indeed, the divide between prokaryotes and eukaryotes is the biggest known evolutionary discontinuity. What allows this increase in complexity? A consensus seems to emerge that the answer lies in energy. It was the acquisition of mitochondria that allowed more energy per gene available for cells (67⇓–69), which, in turn, allowed experimentation with a higher number of genes. This change was accompanied by a more K-selected lifestyle relative to the prokaryotes (70) and optimization for lower death rates (71).

Order of Appearance of Phagocytosis and Mitochondria.
There is no space here to enter the whole maze of the recent debate about the origin of the eukaryotic cells; suffice it to say that the picture seems more obscure than 20 y ago. I illustrate the situation by two strong competing views: phagocytosis (and associated cellular traits) followed by acquisition of mitochondria (72) and the opposite, the acquisition of mitochondria, followed by the evolution of phagocytosis (68, 69). Phylogeny could in principle tell this difference in order, but the analyses are inconclusive (73). The major argument against the phagocytosis-early scenario is once again energetic. According to this view, the boost provided by mitochondria not only was necessary for the evolution of very complex eukaryotic genomes but also was essential for the origin of the eukaryotic condition (69). It is important to realize that these two claims are different, and that the first is often portrayed to imply the latter, which is wrong. The snag is that “archezoan” protists lack mitochondria. Archezoa were once a high taxonomic rank (1) until it became clear that all known examples have or had mitochondria. This development has dethroned Archezoa and at the same time has weakened the position of the phagocytosis-early hypothesis although the latter step is not a logical necessity (73). The “archezoan niche” admittedly exists (69). So why cannot one imagine an archezoan-like intermediate? An attempted answer is again related to the energy. The genome sizes of prokaryotes and eukaryotes overlap around 10 Mb and around 10,000 genes (66). This is the reason why frequent reference to average genome sizes is irrelevant for the discussion of origins. The overlap suggests that a lineage of prokaryotes could have evolved a small but sufficient preeukaryotic genome without mitochondria. If not, why not? Here it is: “the energetic cost for the de novo ‘invention’ of complex traits like phagocytosis must far exceed the costs of simply inheriting a functional system” (ref. 69, p. ) and “it must take many more than the total number of genes that are required in the end. Ten times as many?” (ref. 69, p. 35). If the argument holds, then it should hold in principle for any complex eukaryotic trait (mitosis and meiosis, nucleus, cilia, etc.), and indeed for any complex prokaryotic trait (photosynthesis, multicellularity with fruiting bodies, ribosomes, flagella) as well because both empires experimented with novel gene families and folds relative to what had been there before. There is no theoretical or comparative evidence to support the imagination of such “exuberant evolutionary scaffolding” that would require a transient appearance of a huge number of genes exceeding the final count by up to an order of magnitude. If it is not phagocytosis, then it can only be syntrophy or bacteriovory that allowed the entry of the ancestor of mitochondria. There are comparative concerns with these ideas (73). Archaea are not known to harbor prokaryotic symbionts; only eubacteria harbor (rarely) other eubacteria so the appropriate cross-domain analogy is missing. The same holds for known cases of syntrophy. Moreover, there is no example of a relevant cross-domain syntrophic endosymbiosis. However, it is logically true that it is not necessary for a prokaryote to get into another prokaryote by phagocytosis, but it is equally true that one does not need mitochondria for phagocytosis. Archaea have a cytoskeleton and can even fuse their cells , and there is the undeniable ecological advantage of the phagotrophic niche. Theoretical (72, 74) and phylogenetic (75) considerations are consistent with the idea of a primitively phagotrophic, but otherwise archaeal, host cell [see SI Text, Possible Advantages of Indigestion for a discussion of possible early advantages of not digesting the mitochondrial ancestor, through either benefiting from its photosynthesis (76) or farming (77) by the host cell].

The Nucleocytoplasm and Meiotic Sex.
The origin of the nucleocytoplasm cannot be considered in detail here, but there are two novel, important points to mention. One is that the breaking up of the tight prokaryotic genome organization was presumably due to the invasion of self-splicing introns from mitochondria (68, 78), followed by the evolution of the spliceosome. This transformation would have been impossible unless the protoeukaryote evolved sexual recombination rather early: asexual genomes are a challenge to the spread of selfish genetic symbionts. Meiosis is a shared ancestral character state in eukaryotes (79). As testified by halobacteria, a form of fusion–recombination–fission cycle may have been strictly speaking the first (80, 81). Rather than a separate major transition, meiosis and syngamy seem to be better regarded as a coevolving form of maintenance or transformation of an emerging higher-level evolutionary unit. The other component of the genetic revolution is the emergence of the nucleus itself, from which the name eukaryote is derived. The evolution of introns and eukaryotic gene regulation would have been impossible without the spatial separation of transcription and translation (82). Without the nucleus the genome expansion allowed by the mitochondrial extra energy could not have been realized. The division of labor between cytoplasm in eukaryotes is as important as that between nucleic acids and proteins in prokaryotes: both are enabling constrains.
Several people have questioned the validity of eukaryotic sex as a separate major transition. Although it is true that, during sex, two individuals are needed instead of one (1) and that they share the benefits equally (83), giving it an egalitarian flavor (18), there are two heavy counterarguments: mating pairs do not become parts in the further hierarchy (like cells, for example) and they do not give rise to mating pairs as propagating units (83). The equal sharing of benefits can be realized through haploid or diploid offspring. Enduring diploidy is an optional consequence of sex that arose in certain lineages independently. Now, it seems that the origin of sex is coincident with the origin of the eukaryotic cells, and, in a loose form, it may have preceded it as an archaeal legacy. Whether demoting sex from the major transitions remains justified or not time will tell: we need an updated, detailed scenario for the very origin of the eukaryotic cell. It could be that some stages of the origin of meiosis preceded, others were coincident, and the remaining once followed the acquisition of mitochondria—we do not know. However, just as the prokaryotic stage as we know it may not have been established and maintained without horizontal gene transfer, the eukaryotic condition may never have arisen and been maintained without evolving meiosis.

Dynamics and Levels of Selection.
Curiously little modeling has been done on eukaryotic origins. The stochastic corrector model (Fig. S1C) was published first as applied to a eukaryotic host with two types of asynchronously dividing, complementarily essential organelles, such as mitochondria and plastids (10), and the relation to the origin of protocells by creating shared interests was noted (13, 84). However, mitochondria are much older than plastids so a stage of two types of unregulated and competing primitive organelles may have never existed. However, the stochastic-corrector principle works also with one host and one unsynchronized symbiont just as well. Viewed carefully, the origin of the eukaryotic cell is a prime example of repeated, and sometimes recursive, egalitarian transitions: the origins of mitochondria, meiosis and syngamy, and plastids are variations on this theme.

The Second Eukaryotic Transition: Plastids
Repeated and Recursive Transitions. The origin of plastids is less controversial than the earlier case of the mitochondrion. It now seems that, although in many ways the transition to plastids is analogous to that of mitochondria, the former came much later in an already well-established eukaryotic cell (there are several eukaryotic lineages that do not seem to have had plastids ever). These considerations justify the promotion of plastids to major transition rank in Table 1. There is a further important difference: In contrast to plastids, there are no secondary and tertiary mitochondria. Although it seems that all plastids go back to the same stock of endosymbiotic cyanobacteria, it happened recursively that a eukaryotic cell enslaved another eukaryotic cell because of its photosynthetic potential (76, 85). It is puzzling why we have not seen the analogous case of a protist with archezoan features acquire a second mitochondrion of either pro- or eukaryotic origin (such a discovery would be fascinating). The membrane structure, inheritance, and import mechanisms of nonprimary plastids are complex (76). Recent data indicate that Paulinella might represent a repeated, independent origin of a primary plasmid by the engulfment of a cyanobacterium by an amoeboid cell. This new primary endosymbiosis happened ∼60 million years ago and resulted in a novel way of protein retargeting into the plastid through the Golgi (86).

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6Eukaryotic cells, and their origin Empty Re: Eukaryotic cells, and their origin Thu Jul 30, 2020 4:38 pm


Bioenergetics Constraints on Prokaryotic Cells

Lane has discovered that bioenergetics constraints keep bacterial and archaeal cells trapped at their current size and complexity. Key to discovering this constraint is a metric Lane devised called Available Energy per Gene (AEG). It turns out that AEG in eukaryotic cells can be as much as 200,000 times larger than the AEG in prokaryotic cells. This extra energy allows eukaryotic cells to engage in a wide range of metabolic processes that support cellular complexity. Prokaryotic cells simply can’t afford such processes.

An average eukaryotic cell has between 20,000 to 40,000 genes; a typical bacterial cell has about 5,000 genes. Each gene encodes the information the cell’s machinery needs to make a distinct protein. And proteins are the workhorse molecules of the cell. More genes mean a more diverse suite of proteins, which means greater biochemical complexity.

So, what is so special about eukaryotic cells? Why don’t prokaryotic cells have the same AEG? Why do eukaryotic cells have an expanded repertoire of genes and prokaryotic cells don’t?

In short, the answer is: mitochondria.

On average, the volume of eukaryotic cells is about 15,000 times larger than that of prokaryotic cells. Eukaryotic cells’ larger size allows for their greater complexity. Lane estimates that for a prokaryotic cell to scale up to this volume, its radius would need to increase 25-fold and its surface area 625-fold.

Because the plasma membrane of bacteria is the site for ATP synthesis, increases in the surface area would allow the hypothetically enlarged bacteria to produce 625 times more ATP. But this increased ATP production doesn’t increase the AEG. Why is that?

The bacteria would have to produce 625 times more proteins to support the increased ATP production. Because the cell’s machinery must access the bacteria’s DNA to make these proteins, a single copy of the genome is insufficient to support all of the activity centered around the synthesis of that many proteins. In fact, Lane estimates that for bacteria to increase its ATP production 625-fold, it would require 625 copies of its genome. In other words, even though the bacteria increased in size, in effect, the AEG remains unchanged.


Figure 2: ATP Production at the Cell Membrane Surface. Image credit: Shutterstock

Things become more complicated when factoring in cell volume. When the surface area (and concomitant ATP production) increase by a factor of 625, the volume of the cell expands 15,000 times. To satisfy the demands of a larger cell, even more copies of the genome would be required, perhaps as many as 15,000. But energy production tops off at a 625-fold increase. This mismatch means that the AEG drops by 25 percent per gene. For a genome consisting of 5,000 genes, this drop means that a bacterium the size of a eukaryotic cell would have about 125,000 times less AEG than a typical eukaryotic cell and 200,000 times less AEG when compared to eukaryotes with genome sizes approaching 40,000 genes.

Bioenergetic Freedom for Eukaryotic Cells

Thanks to mitochondria, eukaryotic cells are free from the bioenergetic constraints that ensnare prokaryotic cells. Mitochondria generate the same amount of ATP as a bacterial cell. However, their genome consists of only 13 proteins, thus the organelle’s ATP demand is low. The net effect is that the mitochondria’s AEG skyrockets. Furthermore, mitochondrial membranes come equipped with an ATP transport protein that can pump the vast excess of ATP from the organelle interior into the cytoplasm for the eukaryotic cell to use.

To summarize, mitochondria’s small genome plus its prodigious ATP output are the keys to eukaryotic cells’ large AEG.

Of course, this raises a question: Why do mitochondria have genomes at all? Well, as it turns out, mitochondria need genomes for several reasons (which I’ve detailed in previous articles).

“Why Do Mitochondria Have DNA?”
“Mitochondrial Genomes: Evidence for Evolution or Creation?”
“Mitochondria’s Deviant Genetic Code: Creation or Evolution?”
Other features of mitochondria are also essential for ATP production. For example, cardiolipin in the organelle’s inner membrane plays a role in stabilizing and organizing specific proteins needed for cellular energy production.

From a creation perspective it seems that if a Creator was going to design a eukaryotic cell from scratch, he would have to create an organelle just like a mitochondrion to provide the energy needed to sustain the cell’s complexity with a high AEG. Far from being an evolutionary “kludge job,” mitochondria appear to be an elegantly designed feature of eukaryotic cells with a just-right set of properties that allow for the cellular complexity needed to sustain complex multicellular life. It is eerie to think that unguided evolutionary events just happened to traverse the just-right evolutionary path to yield such an organelle.

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