Eukaryotes, and their origin

Origin of eukaryotes

https://reasonandscience.catsboard.com/t1410-eukaryotic-cells-and-their-origin



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



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. 3 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).

1) http://rstb.royalsocietypublishing.org/content/royptb/370/1678/20140333.full.pdf
2) https://reasonandscience.catsboard.com/t1410-origin-of-eukaryotes#4082
3) http://www.ncbi.nlm.nih.gov/pubmed/20844558
4. https://reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2019/05/01/why-mitochondria-make-my-list-of-best-biological-designs

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



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) .



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)



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)
2) http://www.uncommondescent.com/intelligent-design/genomics-and-the-irreducible-nature-of-eukaryote-cells/

“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.

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.

http://www.nature.com/nature/journal/v440/n7084/full/nature04546.html

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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http://www.pnas.org/content/112/33/10104.full

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.

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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.

https://reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2019/05/01/why-mitochondria-make-my-list-of-best-biological-designs

The Long and Winding Road to Eukaryotic Cells
https://www.the-scientist.com/features/the-long-and-winding-road-to-eukaryotic-cells-70556

Eugene V. Koonin (2015): 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 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 mechanisms rather 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. 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: 

C. G. Kurland: Genomics and the Irreducible Nature of Eukaryote Cells (2006): Data from many sources give no direct evidence that eukaryotes evolved by genome fusion between archaea and bacteria. Because their cells appear simpler, prokaryotes have traditionally been considered ancestors of eukaryotes. 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. 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  (Orthologs are genes in different species that evolved from a common ancestral gene by speciation) 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, hypotheses that attribute eukaryote origins to 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 origins. 2

albeit followed by a swift refutation by Eugene V. Koonin (2007):  The statement that “[e]ukaryote proteins that are rooted in the bacterial or in archaeal clusters are few and far between” is inaccurate. The genomes of both yeast and humans harbor many hundreds of proteins that have readily identifiable homologs among α-proteobacteria but not among archaebacteria, and vice versa. They opine that “t is an attractively simple idea that a primitive eukaryote took up the endosymbiont/mitochondrion by phagocytosis,” yet all testable predictions of that idea have failed. By contrast, examples of prokaryotes that live within other prokaryotes show that prokaryotes can indeed host endosymbionts in the absence of phagocytosis, as predicted by competing alternative theories. They misattribute the notion that a eukaryotic “raptor” phagocytosed the mitochondrion to Stanier and van Niel’s classical paper, which does not mention mitochondrial origin, and to de Duve’s 1982 exposé, which argues for the endosymbiotic origin of microbodies while mentioning “alleged symbiotic adoption” of mitochondria in passing, but without mentioning phagocytosis. Their references and are misattributed as examples of “fusion” hypotheses; indeed, they indiscriminately label views on eukaryote origins that differ from their own as fusion hypotheses.Finally, and most disturbing, if contemporary eukaryotic cells are truly of “irreducible nature,” as Kurland et al.’s title declares, then no stepwise evolutionary process could have possibly brought about their origin, and processes other than evolution must be invoked. Is there a hidden message in their paper? 

which got another response by C. G. KURLAND: OUR VIEW IS THAT CELLULAR AND MOLECULAR biology, especially genomics, reveals signs of an ancient complexity of the eukaryotic cell. This new information was not available to older hypotheses for eukaryote origins; they were answering questions that were incompletely formulated. Our primary conclusions regarding the ancestral complexity of the eukaryote cell microsporidian and the subcellular location of its eukaryote signature proteins (ESPs). Even though Microsporidian genomes are among the most heavily reduced in eukaryotes, they still have many eukaryote signature proteins ESPs. An anaerobic endoparasitic lifestyle (parasites that live in the tissues and organs of their hosts) has reduced their mitochondria to mitosomes and allowed the characteristic proteins of phagocytosis to be lost. Nevertheless, it is striking that characteristic ESPs are found throughout the cell; nothing in this picture suggests they are chimeric descendents of archaeal and bacterial ancestors. 3

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. However, advances in 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. The radical alternative to the elusive archezoa is offered by symbiogenetic scenarios of eukaryogenesis according to which archezoa, i.e. primary amitochondrial eukaryotes, have never existed, and the eukaryotic cell is the product of a symbiosis

between two prokaryotes. Comparative genomic analysis clearly demonstrates that eukaryotes possess two distinct sets of genes, one of which shows phylogenetic affinity with homologues from archaea, whereas the other one includes genes affiliated with bacterial homologues (apart from these two classes, there are many eukaryotic genes of uncertain provenance). The eukaryotic genes of apparent archaeal descent encode, primarily, proteins involved in information processing (translation, transcription, replication, repair), whereas the genes of inferred bacterial origin encode mostly proteins with ‘operational’ functions such as metabolic enzymes, components of membranes and other cellular structures and others. Notably, altogether, the number of eukaryotic protein-coding genes of bacterial origin exceeds the number of ‘archaeal’ proteins about threefold. Thus, although many highly conserved, universal genes of eukaryotes indeed appear to be of archaeal origin, the archaeo-eukaryotic affinity certainly does not tell the entire story of eukaryogenesis, not even most of that story if judged by the proportions of genes of apparent archaeal and bacterial descent.

Although several symbiogenetic scenarios that differ in terms of the proposed partners and even the number of symbiotic events involved have been proposed, the simplest, parsimonious one that accounts for both the ancestral presence of mitochondria in eukaryotes and the hybrid composition of the eukaryotic gene complement involves engulfment of an α-proteobacterium by an archaeon. Under this scenario, a chain of events has been proposed that leads from the endosymbiosis to the emergence of eukaryotic innovations such as the endomembrane system, including the nucleus and the cytoskeleton. Subsequently, argument has been developed that the energy demand of a eukaryotic cell that is orders of magnitude higher than that of a typical prokaryotic cell cannot be met by means other than utilization of multiple ‘power stations’ such as the mitochondria.

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. Although bacterial endosymbionts of certain proteobacteria have been described, such a relationship appears to be a rarity. By contrast, in many unicellular eukaryotes, such as amoeba, engulfment of bacterial cells is routine due to the phagotrophic lifestyle of these organisms. The apparent absence of phagocytosis in archaea and bacteria prompted the reasoning that the host of the proto-mitochondrial endosymbiont was a primitive phagotrophic eukaryote, which implies the presence of an advanced endomembrane system and cytoskeleton. Thus, argument from cell biology seemed to justify rescuing the archezoan scenario, the lack of positive evidence notwithstanding.

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. 3




1. Eugene V. Koonin: Origin of eukaryotes from within archaea, archaeal eukaryote and bursts of gene gain: eukaryogenesis just made easier?  9 June 2015
2. C. G. Kurland: Genomics and the Irreducible Nature of Eukaryote Cells 19 MAY 2006
3. Eugene V. Koonin: The Evolution of Eukaryotes 27 APRIL 2007

Eukaryotic cells

Eukaryotic cells are one of the two primary types of cells that make up all life on Earth (the other being prokaryotic). Eukaryotes encompass a wide variety of organisms, including all plants, animals, fungi, and many types of single-celled organisms. Here's an overview of eukaryotic cells: Unlike prokaryotic cells, eukaryotic cells have a nucleus, which is enclosed by a nuclear envelope. The nucleus contains the cell's DNA, which is organized into chromosomes.
Eukaryotic cells are characterized by having various specialized structures within the cell, each enclosed by its own membrane. These include the endoplasmic reticulum, Golgi apparatus, mitochondria, chloroplasts (in plants and algae), and more. Cell Membrane (Plasma Membrane): A phospholipid bilayer that separates the cell's interior from its environment and regulates the transport of substances in and out of the cell. Embedded in the cell membrane, they allow cells to communicate with each other and respond to external signals. Eukaryotic cells can reproduce both sexually (with meiosis leading to the formation of gametes) and asexually (with mitosis creating genetically identical daughter cells). Eukaryotic cells show tremendous diversity, forming the basis for complex multicellular organisms like plants and animals as well as a myriad of single-celled organisms. Their internal complexity allows for specialized functions and adaptations to a wide range of environments. Eukaryotic cells are complex structures with distinct organelles and processes that allow them to function efficiently and adapt to various environments. Their evolution marked a significant turning point in the history of life, paving the way for the diverse array of species we see today.

List of the structures typically exclusive to, or with unique characteristics in, animal cells in alphabetical order

1. Adherens Junctions: Connect actin filaments of one cell with those of neighboring cells, or to the ECM.
2. Axon Hillock: The region where the axon arises from the neuron's cell body. It's the site where action potentials are initiated.
3. Cell Junctions: Structures in multicellular animals that allow cells to connect and communicate. These include gap junctions, tight junctions, and desmosomes.
4. Centrosome: A cellular structure crucial for the organization of microtubules during cell division. Typically contains two centrioles in animal cells.
5. Desmosomes: Anchoring junctions holding cells together, functioning somewhat like snaps or zippers.
6. Extracellular Matrix (ECM): Though found outside the cell, it's essential for cellular functions. Animal cells secrete fibrous proteins like collagen into the ECM for structural support.
7. Flagella: Tail-like structures, primarily seen in sperm cells, enabling movement. Different in composition from bacterial flagella.
8. Focal Adhesions: Specialized structures where cells in tissues adhere to the ECM components. Internally linked to actin filaments.
9. Gap Junctions: Allow for direct communication between the cytoplasm of adjacent animal cells, facilitating the transfer of ions and small molecules.
10. Hemidesmosomes: Link intermediate filaments in a cell to the extracellular matrix, anchoring at the basal layer of epithelial cells.
11. Intermediate Filaments: Offer mechanical support to cells and help in maintaining their shape.
12. Lamellipodia and Filopodia: Protrusions at the edge of migrating cells, containing a dense mesh of actin filaments.
13. Lysosomes: Organelles filled with enzymes that help in breaking down cellular waste into usable materials.
14. Microvilli: Extensions of the plasma membrane that enhance the surface area of cells, mainly assisting absorption in animal cells.
15. Neurofilaments: Intermediate filaments specific to neurons, offering structural support.
16. Neurotransmitter Receptors: Specialized protein structures in neurons that receive signals across the synapse.
17. Peroxisomes: Enzyme-containing structures which break down fatty acids and amino acids, subsequently producing hydrogen peroxide.
18. Secretory Vesicles: Vesicles containing substances like hormones and neurotransmitters that are expelled from the cell.
19. Synaptic Vesicles: Hold various neurotransmitters to be released at the synapse in response to an action potential.
20. Tight Junctions: Specialized connections between neighboring epithelial cells that create a barrier restricting movement of substances.

Other structures unique to animal cells or having specialized functions in them:

21. Caveolae: Small, flask-shaped invaginations in the plasma membrane that participate in endocytosis and signal transduction.
22. Stereocilia: Not true cilia but rather long microvilli. Found in the inner ear, they play a crucial role in detecting sound and balance.
23. Contractile Vacuoles: While primarily found in some protozoa, these structures aid in osmoregulation, expelling excess water out of the cell.

This list provides a comprehensive look at structures predominantly found in animal cells, bearing in mind the distinctions in function or structure from similar entities in other cell types. It's essential to emphasize that, while these structures are present or predominant in animal cells, some might have homologs or analogs in non-animal eukaryotic cells with different functions or structural features. While some of these structures, like the flagella, can be found in other organisms, their composition, structure, and function in animal cells are distinct.


Proteins families of eukarya

1. Actin Family: Cytoskeletal proteins involved in muscle contraction, cell motility, and maintenance of cell shape.
2. Tubulin Family: Constitutes microtubules, vital for cell division, intracellular transport, and maintaining cell shape.
3. Histone Family: Proteins around which DNA wraps, playing a role in gene regulation.
4. G-Protein Family: Involved in transmitting signals from various stimuli outside a cell to its interior.
5. Immunoglobulin Superfamily (IgSF): Includes a variety of cell surface proteins including antibodies, T-cell receptors, and various adhesion molecules.
6. Kinase Family: Enzymes that transfer phosphate groups, playing key roles in signaling pathways.
7. Phosphatase Family: Enzymes that remove phosphate groups, counterbalancing the action of kinases.
8. Heat Shock Proteins (HSPs): Act as chaperones assisting in protein folding and protection against stress.
9. Protease Family: Enzymes that break down proteins.
10. Helicase Family: Enzymes that unwind DNA or RNA helices, essential for replication, transcription, and repair.
11. ATPase Family: Enzymes that hydrolyze ATP, driving various biological processes.
12. Transporter Family: Involved in the movement of ions, small molecules, and macromolecules across cell membranes.
13. Ion Channel Family: Facilitate the passive movement of ions across cell membranes.
14. GTPase Family: Hydrolyze GTP and are involved in signal transduction.
15. Transcription Factor Family: Proteins that regulate gene expression by binding to specific DNA sequences.
16. Receptor Family: Proteins that receive and transduce signals, often spanning the cell membrane.
17. Ligase Family: Enzymes that facilitate the joining of two molecules.
18. Topoisomerase Family: Enzymes that change the degree of supercoiling of DNA.
19. Cyclin Family: Proteins that regulate the cell cycle in partnership with cyclin-dependent kinases (CDKs).
20. Motor Protein Family: Proteins that convert chemical energy into mechanical work, including myosin, dynein, and kinesin.
21. Adaptin Family: Involved in vesicle formation and protein sorting.
22. Annexin Family: Calcium-dependent phospholipid-binding proteins with diverse roles, including vesicle trafficking and cell signaling.
23. Bcl-2 Family: Regulates programmed cell death, with members promoting either cell survival or apoptosis.
24. Cadherin Family: Mediates calcium-dependent cell-cell adhesion in tissues.
25. Calmodulin and EF-hand Protein Family: Calcium-binding proteins involved in various calcium-mediated signaling pathways.
26. Caspase Family: Cysteine-dependent proteases that play key roles in apoptosis and inflammation.
27. Claudin Family: Integral membrane proteins crucial for the formation of tight junctions in epithelial and endothelial cell layers.
28. DEAD box Helicase Family: RNA helicases involved in multiple processes including ribosome biogenesis, RNA splicing, and translation initiation.
29. Fibronectin Type III Domain Family: Found in various proteins involved in cell adhesion and receptor signaling.
30. Glycosyltransferase Family: Enzymes that catalyze the transfer of sugar moieties to various substrates.
31. Hedgehog Protein Family: Involved in intercellular signaling during development.
32. Homeobox (HOX) Family: Transcription factors that regulate the development of body structures.
33. Integrin Family: Transmembrane receptors that facilitate cell-extracellular matrix adhesion.
34. Interferon Family: Proteins involved in defense against viral infections.
35. Keratin Family: Intermediate filament proteins present in epithelial cells.
36. Krüppel-like Factor (KLF) Family: Transcription factors involved in a wide range of cellular processes.
37. Lectin Family: Proteins that bind specifically to certain sugars and can modify other proteins or lipids.
38. Matrix Metalloproteinase (MMP) Family: Enzymes involved in the degradation of extracellular matrix.
39. Pentatricopeptide Repeat (PPR) Family: RNA-binding proteins primarily found in plants, involved in RNA editing.
40. Perilipin Family: Phosphoproteins that coat lipid droplets in adipocytes and other cells.
41. RAS Protein Family: Small GTPases involved in cell growth, differentiation, and survival.
42. SERCA Family: Sarco/endoplasmic reticulum Ca^2+-ATPases involved in calcium pumping.
43. Sirtuin Family: NAD-dependent deacetylases involved in cellular regulation.
44. SNARE Protein Family: Crucial for vesicle fusion with target membranes.
45. SOCS Family: Suppressor of cytokine signaling proteins, regulate cytokine responses.
46. Src Family Kinases (SFKs): Involved in the regulation of growth and differentiation of eukaryotic cells.
47. STAT Protein Family: Signal transducer and activator of transcription proteins, involved in cell growth, differentiation, and apoptosis.
48. Tetraspanin Family: Membrane proteins that play roles in cell adhesion, motility, and proliferation.
49. TRP Channel Family: Transient receptor potential channels involved in sensation (e.g., temperature, pressure).
50. Tumor Necrosis Factor (TNF) Family: Cytokines involved in cell differentiation, proliferation, and death.
51. Ubiquitin-Proteasome System: Responsible for protein degradation in the cell.
52. WD Repeat Protein Family: Proteins with repeating units often facilitating protein-protein interactions.
53. Zinc Finger Protein Family: One of the largest families of transcription factors in eukaryotic genomes.
54. Beta-Barrel Outer Membrane Protein Family: Forms channels for nutrient uptake and waste removal in mitochondria and chloroplasts.
55. Short Chain Dehydrogenase/Reductase (SDR) Family: Large family of enzymes involved in metabolism.
56. P-Type ATPase Family: Transmembrane proteins that transport a variety of different ions across membranes.
57. Ankyrin Repeat Family: Mediate protein-protein interactions in very diverse families of proteins.
58. BTB Domain Family: Proteins involved in protein-protein interactions.
59. RNA Recognition Motif (RRM) Family: Common RNA-binding domain in many RNA-binding proteins.
60. Cytochrome P450 Family: Involved in the synthesis of cholesterol, steroids, and other lipids.
61. SET Domain Protein Family: Involved in modulating chromatin structure and mediating epigenetic memory.
62. PAS Domain Protein Family: Serves as a signal sensor in various signaling proteins.
63. PDZ Domain Protein Family: Play a role in anchoring receptors and channels to the cytoskeleton.
64. Helix-Turn-Helix (HTH) Family: Common in DNA binding proteins like transcription factors.
65. HLH Protein Family: Involved in protein-protein interactions and have been implicated in the regulation of gene expression.
66. Leucine Zipper Family: Involved in the formation of specific DNA-protein and protein-protein interactions.
67. F-Box Protein Family: Involved in phosphorylation-dependent ubiquitination processes.
68. Rho Family: Small GTPases that regulate cytoskeletal dynamics and organization.
69. PH Domain Protein Family: Play roles in intracellular signaling pathways.
70. SH2 Domain Protein Family: Involved in several cellular processes including signal transduction, cytoskeletal reorganization, and membrane trafficking.



References

●Koonin, E.V. (2015). Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier? Philos Trans R Soc Lond B Biol Sci, 370(1678), 20140333. Link. (Eugene V. Koonin delves into the topic of eukaryogenesis and explores the theory that eukaryotes may have originated from within the archaea domain. The study sheds light on the possible evolutionary steps leading to the emergence of eukaryotes.)
●Katz, L.A. & Grant, J.R. (2015). Taxon-rich phylogenomic analyses resolve the eukaryotic tree of life and reveal the power of subsampling by sites. Systematic Biology, 64(3), 406-415. Link. (This research undertakes a phylogenomic analysis to shed light on the eukaryotic tree of life, providing insights into LECA.)
●Imachi, H., Nobu, M.K., Nakahara, N., Morono, Y., Ogawara, M., Takaki, Y., ... & Takai, K. (2020). Isolation of an archaeon at the prokaryote–eukaryote interface. Nature, 577(7791), 519-525. Link. (This study discusses the discovery of a new archaeon that provides clues about the nature of the prokaryote-eukaryote boundary and the origins of eukaryotes.)
●Eme, L., Spang, A., Lombard, J., Stairs, C.W., & Ettema, T.J.G. (2017). Archaea and the origin of eukaryotes. Nature Reviews Microbiology, 15(12), 711-723. Link. (This review article explores the role of archaea in the origins of eukaryotes, bringing together various lines of evidence to understand the relationship between these two domains and the nature of LECA.)
●O’Malley, M.A., Leger, M.M., Wideman, J.G., & Ruiz-Trillo, I. (2019). Concepts of the last eukaryotic common ancestor. Nature Ecology & Evolution, 3, 338–344. Link. (This perspective piece delves into the concept of the last eukaryotic common ancestor (LECA) and discusses its importance and role in the evolutionary history of eukaryotes.)
●López-García, P., & Moreira, D. (2015). Open Questions on the Origin of Eukaryotes. Trends in Ecology & Evolution, 30(11), 697-708. Link. (This review article addresses unresolved questions pertaining to the origin of eukaryotes, discussing various hypotheses and the evidence supporting them.)

Organelles used in Animal Cells

All animals, plants, fungi, and many unicellular organisms (Protists) are eukaryotes

Membrane-Bound Organelles in animal cells

1. Acidocalcisomes: Universally distributed organelles that are involved in the storage of polyphosphates and play crucial roles in pH, calcium, and osmotic homeostasis.
2. Acrosome: Found in sperm cells, this structure contains enzymes that help the sperm penetrate the egg during fertilization.
3. Anammoxosome: Specialized organelle in bacteria that carry out anaerobic ammonia oxidation.
4. Annulate lamellae: Stacks of membranous structures found in the cytoplasm, having pore complexes similar to those in the nuclear envelope.
5. Autophagosomes: Organelles involved in the degradation and recycling process of cellular components through autophagy.
6. Cilia and Flagella: Projections from the cell, cilia are short and numerous while flagella are longer. Both used for movement.
7. Contractile Vacuole: Regulates the quantity of water and ions within cells, mainly in protists.
8. Endocytic Vesicles: Vesicles formed at the plasma membrane to allow the intake of large molecules.
9. Endoplasmic Reticulum (ER): A network of membranous sacs and tubes. Rough ER is involved in protein synthesis, while Smooth ER is involved in lipid synthesis and other functions.
10. Endosomes: Involved in sorting and recycling materials brought into the cell through endocytosis.
11. Exosome: Small vesicle containing cellular waste.
12. Flagella: Whip-like structures that protrude from the body of a cell and provide mobility.
13. Glycosome: Organelle in which glycolysis occurs.
14. Golgi Apparatus: Modifies, sorts, and packages proteins and lipids for transport.
15. Hydrogenosome: Energy-producing organelle in some anaerobic microbes.
16. Lamellar bodies (or lamellar granules): Found in type II pneumocytes in the lungs, these organelles store and secrete surfactant, which prevents the alveoli from collapsing.
17. Lipid Droplets: Organelles primarily involved in the storage of neutral lipids.
18. Lysosomes: Organelles containing enzymes that digest cellular waste.
19. Lysosome-related Organelles (LROs): Specialized lysosomes found in certain cells like melanocytes and immune cells with unique functions specific to the cell type.
20. Magnetosome: Bacterial organelle containing magnetite or greigite crystals, aiding in navigation.
21. Melanosome: Organelle in which melanin biosynthesis and storage occurs.
22. Mitochondria: Responsible for ATP production.
23. Multivesicular bodies (MVBs): Intracellular trafficking organelles formed as endosomes mature. They contain many smaller vesicles inside.
24. Nuclear Envelope: A membrane structure that surrounds the nucleus.
25. Nucleolus: Found within the nucleus, responsible for ribosomal RNA synthesis.
26. Nucleus: Contains the genetic material (DNA) of the cell.
27. Peroxisomes: Organelles that contain enzymes to break down fatty acids, amino acids, and detoxify certain chemicals.
28. Phagosome: Vesicle formed around a particle engulfed by a phagocyte via phagocytosis.
29. Rough Endoplasmic Reticulum: Involved in protein synthesis and membrane production.
30. Secretory Vesicles: Vesicles that transport and release substances outside a cell by exocytosis.
31. Sarcoplasmic Reticulum: A specialized ER in muscle cells, involved in calcium ion storage.
32. Smooth Endoplasmic Reticulum: Involved in lipid synthesis, detoxification, and calcium ion storage.
33. Synaptic Vesicles: Store neurotransmitters in neuron ends for release.
34. Transport Vesicles: Involved in transporting materials within the cytoplasm.
35. Trans-Golgi Network: A section of the Golgi involved in modifying and packaging proteins.
36. T-tubules (Transverse tubules): Extensions of the cell plasma membrane that penetrate into the center of skeletal and cardiac muscle cells.
37. Vesicles: Small membrane-bound sacs that store and transport substances within the cell.
38. Weibel-Palade Bodies: Storage granules in endothelial cells, containing von Willebrand factor and other proteins.
39. Primary Cilium: A solitary, non-motile cilium that protrudes from the surface of nearly every mammalian cell. It has sensory capabilities.
40. Microvillar Channels: Found on the microvilli of specialized cells such as the epithelial cells in the intestine; these are involved in nutrient absorption.
41. Mucociliary Clearance Apparatus: Found in the respiratory tract, this apparatus utilizes coordinated cilia movements to move mucus, and the particles trapped in it, out of the lungs.
42. Caveolae: Invaginations in the plasma membrane associated with lipid rafts, involved in endocytosis and transcytosis processes.
43. Vaults: Large ribonucleoprotein particles that may have roles in intracellular transport.
44. Residual Body: Contains the remains of lysosomal digestion, which can sometimes be ejected from the cell.
45. Tricellular Junctions: Specialized regions where three cells meet, which have tight junction proteins to seal the spaces between cells.
46. Lamellar Bodies in Skin: Found in keratinocytes, these organelles release a lipid-rich secretion contributing to the water-repellent properties of skin.

Non-Membrane-Bound Organelles and Structures in animal cells  

1. Actin Filaments: Part of the cytoskeleton that interacts with myosin for muscle contraction and plays a role in cell movement.
2. Basal Body: Anchors cilia and flagella to the cell body.
3. Centrioles: Cylinder-shaped structures involved in cell division in animal cells.
4. Centrosome: Involved in cell division and organization of the microtubules in the cytoskeleton.
5. Coiled Bodies (Cajal Bodies): Nuclear bodies involved in the biogenesis of snRNPs and snoRNPs.
6. Cristae: Folds in the inner membrane of mitochondria.
7. Cytoskeleton: Provides structural support to the cell.
8. Elastoplasts: Organelles containing elastin.
9. Food Vacuole: Vesicle in which ingested particles are digested.
10. Gems (Gemini of coiled bodies): Small nuclear bodies involved in the modification of spliceosomal snRNPs.
11. Histones: Proteins responsible for the structure of chromatin in eukaryotic nuclei.
12. Inclusion Bodies: Granules of storage material within cells.
13. Intermediate Filaments: Cytoskeletal elements providing structural support to cells.
14. Lipid Rafts: Specialized membrane microdomains that compartmentalize cellular processes.
15. Matrix: Internal space of mitochondria.
16. Microfilaments: Fine, thread-like protein fibers made of actin, involved in cell movement and changes in cell shape.
17. Microtubule Organizing Center (MTOC): An area where microtubules are produced.
18. Microtubules: Spiral chains of protein globules that provide structural support and play a role in cell division.
19. Myofibrils: Contractile fibers in muscle cells.
20. Nematocysts: Specialized organelles in cnidarians for capturing prey.
21. Nuclear Lamina: A dense fibrillar network inside the nucleus that provides structural support.
22. Nuclear Matrix: A fibrillar network inside the nucleus that helps organize the chromosomes.
23. Nuclear Pores: Channels in the nuclear envelope that allow materials to move in/out of the nucleus.
24. Nuclear Speckles: Nuclear structures rich in pre-mRNA splicing factors.
25. Nucleoid: The DNA-containing region in prokaryotes.
26. Perinuclear Space: The region between the two bilayers of the nuclear envelope.
27. Pinocytic Vesicles: Vesicles involved in the intake of liquids and dissolved substances.
28. Polar Bodies: Small cells that are the byproduct of meiosis in female gamete development.
29. Polyribosomes (Polysomes): Groups of ribosomes reading a single mRNA simultaneously, thus enhancing the efficiency of translation.
30. Proteasome: Complexes that degrade unneeded or damaged proteins by proteolysis.
31. P-bodies (Processing bodies): Cytoplasmic foci formed by the aggregation of mRNAs and various proteins. Involved in mRNA storage and degradation.
32. Ribosomes: Sites of protein synthesis composed of rRNA and proteins.
33. Septin Filaments: Proteins involved in cell division, particularly cytokinesis.
34. Spindle Apparatus: Consists of microtubules that help segregate chromosomes during mitosis.
35. Residual Body: Contains the remains of lysosomal digestion, which can sometimes be ejected from the cell.
36. Tricellular Junctions: Specialized regions where three cells meet, which have tight junction proteins to seal the spaces between cells.
37. Lamellar Bodies in Skin: Found in keratinocytes, these organelles release a lipid-rich secretion contributing to the water-repellent properties of skin.

Organelles exclusively used in Plant Cells

Plants, as primary producers in many ecosystems, possess a unique cellular machinery that equips them to perform photosynthesis, grow towards the light, and establish strong physical forms to stand against the forces of nature. This complex machinery is composed of both membrane-bound and non-membrane bound organelles, each contributing to the plant's ability to thrive and reproduce.

Membrane-bound Organelles in Plant Cells

1. Amyloplast: An organelle where starch is synthesized and stored.
2. Calciosome: An organelle involved in calcium storage.
3. Chloroplasts: Organelles responsible for photosynthesis, converting light energy into chemical energy.
4. Chromoplast: Organelles responsible for pigment synthesis and storage.
5. Elastichromoplasts: Organelles responsible for storing and synthesizing elastic polymers.
6. Glyoxysome: Specialized peroxisomes that convert fat into sugar.
7. Granum (Grana): A stack of thylakoids within the chloroplast.
8. Leucoplast: A general term for all colorless plastids, involved in synthesis and storage of lipids, proteins, and starches.
9. Plasmalemma: The plasma membrane regulating solute movement.
10. Proplastid: Precursors to other plastids, differentiating based on cellular needs.
11. Tannosome: Organelle where tannins are synthesized.
12. Thylakoid: Membranous structures in the chloroplast for light-dependent reactions.
13. Tonoplast: The membrane enclosing the central vacuole.
14. Vacuole: A large sac responsible for storage and breakdown of substances.

Non-membrane bound Organelles and Components in Plant Cells

1. Apical Meristem: A growth region at root and shoot tips where cells divide rapidly.
2. Axillary Bud: A bud at the junction of a stem and leaf petiole.
3. Bundle Sheath Cells: Specialized cells in C4 plants for the Calvin cycle.
4. Casparian Strip: A barrier band around root endodermal cell walls.
5. Cell Plate: A developing partition forming the cell wall during division.
6. Cell Wall: A rigid layer providing support and protection, made of cellulose.
7. Chlorophyll: The green pigment for photosynthesis.
8. Collenchyma Cells: Supportive cells in young plants.
9. Companion Cells: Specialized phloem cells supporting sieve-tube elements.
10. Cork Cells: Dead cells forming the outer bark in woody plants.
11. Crystal Idioblasts: Cells containing defensive crystals.
12. Cuticle: A waxy layer reducing water loss.
13. Endodermis: The innermost layer of root cortex cells.
14. Epidermis: The outermost cell layer covering the plant.
15. Fibrous Root: A type of root system with thin roots spreading out.
16. Guard Cells: Paired cells regulating stomata.
17. Internode: The segment of a stem between two nodes.
18. Lateral Meristem: A meristem allowing growth in diameter.
19. Lignin: A compound strengthening some plant cell walls.
20. Mesophyll: The inner tissue of a leaf with many chloroplasts.
21. Node: Where leaves or branches attach to a stem.
22. Parenchyma Cells: Fundamental plant tissue involved in various functions.
23. Pericycle: A thin layer of tissue between endodermis and phloem.
24. Perisome: Structures aiding in seed or spore release.
25. Phragmoplast: A structure aiding in cell plate formation during division.
26. Pit Field: Regions where plasmodesmata cluster.
27. Plasmodesmata: Channels enabling communication between cells.
28. Proteoplast: A plant cell without its cell wall.
29. Pulvinus: A motor organ allowing certain plant movements.
30. Raphide: Needle-shaped crystals in plant cells.
31. Sclerenchyma Cells: Cells that provide mechanical support.
32. Stoma (Stomata): Pores on plant surfaces for gas exchange.
33. Stroma: The fluid matrix inside the chloroplast.
34. Tapetum: Nutritive cells nourishing developing pollen grains.
35. Tracheids: Cells in the xylem transporting water and nutrients.
36. Xylem: Vascular tissue transporting water and nutrients.



Organelles exclusively used in Fungi

Fungi have a unique cellular organization and possess some distinct organelles or structures. Here's a list of membrane-bound and non-membrane bound organelles and structures that are exclusively encountered or have specialized roles in fungi:

Membrane-bound Organelles in Fungi

1. Chitosomes: Vesicles that carry chitin synthase, aiding in the synthesis of chitin, a component of the fungal cell wall.
2. Spitzenkörper: A unique organelle located at the fungal hyphal tip, playing a role in polarized growth. It is a vesicle supply center that directs vesicles to the growing tip.
3. Woronin Body: Found in some fungi, especially Ascomycota, it plugs septal pores in response to hyphal wounding, preventing excessive cytoplasmic loss.

Non-membrane bound Organelles and Components in Fungi

1. Septa: Internal cross-walls that divide the fungal hyphae into cells or compartments. However, they usually have pores, allowing cytoplasm and even organelles to move between compartments.
2. Dolipore Septum: A specialized form of septum found in many Basidiomycetes. It consists of a pore flanked by two swollen regions (parenthesomes) and allows the selective movement of organelles and cytoplasm between hyphal compartments.
3. Chitin: A polysaccharide that is a primary component of fungal cell walls. It provides strength and rigidity.
4. Clamp Connection: A specialized structure in some Basidiomycetes that aids in the distribution of nuclei during cell division.

These organelles and structures play vital roles in fungal growth, reproduction, and adaptation to various environments. While some may have analogs or equivalents in other organisms, the structures and roles described above are specific to fungi.

Protists are an incredibly diverse group of eukaryotic microorganisms. While many organelles are shared with other eukaryotes, there are some specialized structures that are more commonly or exclusively found in various protists. Here's a list of membrane-bound and non-membrane bound organelles and structures that are especially pertinent to protists:



Membrane-bound Organelles in Protists

1. Contractile Vacuole: Found in many freshwater protists, this organelle pumps excess water out of the cell to maintain osmotic balance.
2. Pigment Plastids: These are specialized plastids that contain pigments. In photosynthetic protists like dinoflagellates and euglenids, these plastids help capture light energy.
3. Pellicle: A membrane complex in some protists, especially euglenoids, that provides structural support and gives the cell its shape.
4. Mucocysts: Found in ciliates, these are specialized organelles that release a sticky substance to trap predators or prey.
5. Trichocysts: Found in some protists like Paramecium, these are rod-shaped structures that can be discharged in response to stimuli, potentially for defense or capturing prey.
6. Hydrogenosomes: Found in some anaerobic protists, these organelles produce hydrogen gas during metabolism.

Organelles exclusively used in Protists

Non-membrane bound Organelles and Components in Protists

1. Axostyle: A stiff rod-like structure found in some flagellated protists, helping to provide support.
2. Parabasal Body: Associated with the axostyle in some protists, it's believed to be involved in cell structure support.
3. Cytostome: A cell mouth through which some protists ingest food particles.
4. Nucleomorph: Found in some cryptomonads, it's a remnant nucleus from a eukaryotic endosymbiont.
5. Stigma (Eyespot): A light-sensitive organelle found in some green algae and other photosynthetic protists, which helps the organism to move in response to light.
6. Kinetochores: Unique barrel-shaped structures found in some protists, aiding in chromosome separation during cell division.

Protists, due to their diversity, have a wide range of specialized structures and organelles adapted to their various lifestyles, from parasitic to photosynthetic and beyond. The structures listed above represent only a subset of the variety found within this fascinating group of organisms.

This summary is based on a consensus of recent phylogenomic studies. The colored groupings correspond to the current ‘supergroups’. Unresolved branching orders among lineages are shown as multifurcations. Broken lines reflect lesser uncertainties about the monophyly of certain groups. Star symbols denote taxa that were considered as supergroups in early versions of the supergroup model; thus, all original supergroups except Archaeplastida have either disappeared or been subsumed into new taxa. The circles show major lineages that had no molecular data when the supergroup model emerged, most often because they had not yet been discovered. Rappemonads (in parentheses) are placed on the basis of plastid rRNA data only. The putative new major lineages Microheliella and Anaeramoeba are not shown due to the limited evidence that they belong outside all existing groups shown here 1

The eukaryotic supergroups in chronological order of appearance according to the evolutionary timeline:

● Origin of Eukaryotes: The eukaryotic lineage is believed to have originated around 1.5 to 2 billion years ago.

● Hemimastigophora: Known as 'hemimastigotes', these are free-living protozoa with dual rows of flagella. Based on recent phylogenomic analyses, the Hemimastigophora might represent one of the earliest branching eukaryote lineages. Some estimates suggest they diverged around 1.2 to 1.8 billion years ago, though further research is needed to refine this timeline.  Known since the 19th century, 'hemimastigotes' are believed to be free-living protozoa with two flagellar rows. Recent phylogenomic analyses have highlighted their deep evolutionary roots, suggesting that they might be one of the earliest eukaryotic branches.
● Archaeplastida: This supergroup, including the Chloroplastida, Rhodophyta (red algae), and Glaucophyta, emerged following the acquisition of primary plastids from cyanobacteria. Their divergence is believed to have occurred around 1 to 1.5 billion years ago. Encompassing Chloroplastida, Rhodophyta, and Glaucophyta, Archaeplastida is postulated to have a unique evolutionary story. All three lineages are believed to have primary plastids that supposedly originated directly from cyanobacteria. The recent discovery of Rhodelphis, which is claimed to be closely related to red algae, adds another layer of complexity. While the common origin of primary plastids is said to unify Archaeplastida, its exact placement in the evolutionary tree remains a topic of debate.
● Amorphea: Housing the opisthokonts (animals, fungi, and their unicellular relatives) and Amoebozoa (amoeboid protists), the Amorphea likely diverged approximately 900 million to 1.2 billion years ago. This group is said to combine opisthokonts with amoeboid protists of Amoebozoa. Amorphea's lineage also supposedly includes two smaller groups of heterotrophic flagellates: the breviates and the apusomonads. Recent phylogenomic analyses have robustly supported the Amorphea grouping, although the exact position of its root remains a point of contention.
● TSAR (Telonemids, Stramenopiles, Alveolates, and Rhizaria): The core groups of Stramenopiles, Alveolates, and Rhizaria likely diverged from common ancestors around 800 million to 1 billion years ago. The inclusion of Telonemids to form the TSAR clade is based on newer phylogenomic evidence.  Representing a substantial segment of eukaryotic diversity, the TSAR group is thought to have evolved early in the phylogenomic era. Consisting of telonemids, stramenopiles, alveolates, and Rhizaria, it includes entities ranging from microbial algae such as diatoms and dinoflagellates to major seaweeds like kelps and ecologically significant protozoa. Also, numerous protozoan parasites, familiar to many, are claimed to be part of this group. Telonemia, an enigmatic free-living flagellate group with just two known species, is supposedly the sister group to SAR, leading to the recognition of the TSAR grouping. Recent phylogenomic analyses support the prominence of this supergroup in the tapestry of eukaryotic evolution.
● Discoba: Including the Euglenozoa and Heterolobosea groups, the Discoba probably branched off around 750 million to 1 billion years ago. This group, thought to include Euglenozoa, Heterolobosea, Jakobida, and Tsukubamonas, is believed to play a vital role in various ecosystems. Their diverse members, ranging from euglenophyte algae to heterotrophic amoebae and flagellates, supposedly share a common evolutionary origin, as reinforced by multiple phylogenomic analyses.
● Metamonada: Comprising entirely of anaerobic protists, this supergroup likely separated from other eukaryotic lineages between 700 million to 900 million years ago. This group, comprising solely of anaerobic protists, is thought to have a unique place in evolutionary studies. Their lineage supposedly includes free-living protozoa, intestinal symbionts, and various parasites. Despite the challenges in placing them relative to other taxa, phylogenomic analyses have consistently supported their distinction.
● Cryptista: With members like cryptomonads, the divergence time for this supergroup is estimated to be around 700 million to 900 million years ago, though more precise dates are debated. Enclosing cryptomonads, katablepharids, and the recently discovered Palpitomonas, Cryptista has been central to discussions on plastid origin and its spread across eukaryotes. This group supposedly emerged to help scientists understand the intricate web of eukaryotic relationships. Phylogenomic examinations have reinforced the claim of Cryptista's distinct evolutionary path.
● Haptista: Comprising haptophyte algae and centrohelids, the Haptista likely emerged around 600 million to 800 million years ago.Haptista, which comprises haptophyte algae and centrohelids, is believed to hold a significant position in marine ecosystems. Especially the coccolithophorids, like Emiliania huxleyi, are thought to play pivotal roles. On the other hand, centrohelids, free-living protozoa showcasing ray-like pseudopodia, add to the group's diversity. Various phylogenomic studies have backed the distinction of Haptista in the evolutionary storyline.
● CRuMs: As a recently proposed supergroup, the exact divergence timing for CRuMs is less well-defined. Tentative estimates suggest a divergence around 600 million to 800 million years ago. A recently proposed supergroup, CRuMs is believed to have originated somewhere between 600 million to 800 million years ago. Represented by an acronym of its constituent members, it groups together the collodictyonids, Rigifilida, and Mantamonas. These groups, despite their varying basic morphologies, are claimed to have a shared evolutionary pathway, as seen in recent phylogenomic studies.
● Orphan Taxa: The evolutionary timeline for orphan taxa remains uncertain due to the lack of clear phylogenomic placement. Some might have ancient origins similar to Hemimastigophora, while others might have emerged more recently. This category encapsulates several taxa that are yet to find a firm phylogenomic placement. These supposed 'orphan taxa', including entities like Ancoracysta, Picozoa, and malawimonads, are all claimed to be free-living protozoa. Some of them might find connections with established groups in the future, but others might turn out to be distinct lineages with their own evolutionary stories.

These estimates are based on current knowledge and can change with new research findings. The timeline provides a broad overview and should be taken as a generalized representation of eukaryotic evolution. The intricate web of eukaryotic evolution continues to evolve, with recent phylogenomic analyses shedding light on the relationships between these supergroups. The picture remains incomplete, and as science delves deeper, further complexities might emerge, reshaping our understanding of eukaryotic life.

1. Burki, F., Roger, A.J., Brown, M.W., & Simpson, A.G.B. (2020). The New Tree of Eukaryotes. Trends in Ecology & Evolution, 35(1), 43-55. Link. (This comprehensive review redefines our understanding of eukaryotic evolution, shedding light on the intricate relationships between diverse eukaryotic lineages.)

● Findeisen, P., Mühlhausen, S., Dempewolf, S., Hertzog, J., Zietlow, A., Carlomagno, T., & Kollmar, M. (2014). Six Subgroups and Extensive Recent Duplications Characterize the Evolution of the Eukaryotic Tubulin Protein Family. Genome Biology and Evolution, 6, 2274 - 2288. Link. (This paper elaborates on the evolution of the eukaryotic tubulin protein family, emphasizing the significance of subgroups and recent duplications.)

● Velasco, J. (2018). Universal common ancestry, LUCA, and the Tree of Life: three distinct hypotheses about the evolution of life. Biology & Philosophy, 33, 1-18. Link. (Velasco delves into three major hypotheses surrounding the evolution of life, examining universal common ancestry, LUCA, and the Tree of Life.)

● Giulio, M. (2019). The universal ancestor, the deeper nodes of the tree of life, and the fundamental types of primary cells (cellular domains). Journal of Theoretical Biology, 460, 142-143. Link. (This paper investigates the concept of a universal ancestor in conjunction with the deeper nodes of the evolutionary tree and primary cellular domains.)

● O’Malley, M., Leger, M., Wideman, J., & Ruiz-Trillo, I. (2019). Concepts of the last eukaryotic common ancestor. Nature Ecology & Evolution, 3, 338-344. Link. (A comprehensive discussion on the various concepts pertaining to the last eukaryotic common ancestor.)

● Deutekom, E., Snel, B., & Dam, T. (2020). Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes. Briefings in Bioinformatics, 22. Link. (This research benchmarks orthology methods based on phylogenetic patterns established at the foundational level of Eukaryotes.)

● Berkemer, S., & McGlynn, S. (2020). A New Analysis of Archaea–Bacteria Domain Separation: Variable Phylogenetic Distance and the Tempo of Early Evolution. Molecular Biology and Evolution, 37, 2332 - 2340. Link. (This research provides a fresh perspective on the domain separation between Archaea and Bacteria, highlighting the variable phylogenetic distance.)

● Gagler, D., Karas, B., Kempes, C., Goldman, A., Kim, H., & Walker, S. (2021). Scaling laws in enzyme function reveal a new kind of biochemical universality. Proceedings of the National Academy of Sciences of the United States of America, 119. Link. (A groundbreaking paper discussing scaling laws in enzyme function, suggesting a novel form of biochemical universality.)

● Craig, J.M., Kumar, S., & Hedges, S.B. (2023). The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen. Front. Bioinform., 3. Link. (This research explores the relationship between the origin of eukaryotes, increased complexity, and the rise in atmospheric oxygen levels, suggesting a synchronicity among these events.)