The eukaryotic cell

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Eukaryotic cells (Figure 3) are often large in size and have a complex structure with a true cytoskeleton (microtubules of tubulins, actin microfilaments, etc.) and a system of internal membranes delimiting numerous organelles: nucleus, endoplasmic reticulum, Golgi apparatus, early endosomes, late endosomes or multivesicular bodies, lysosomes, vacuoles, peroxisomes, inclusion bodies, mitochondria… They are always surrounded by a single plasma membrane containing varying levels of sterols. Structures located under the membrane (the cortex) or outside (wall, thecae, frustules, shells, etc.) often strengthen the membrane and give it a well-defined shape. The cytoskeleton (Box 1) not only reinforces the cell to enable it to resist external attacks, but also allows the intracellular movements of various materials required by the large size and compartmentalisation of the eukaryotic cell, including vesicular trafficking (Figure 4), as well as the movements of the cell, either via the pseudopodia (Figure 5) based on the actin/myosin cytoskeleton or the flagella or cilia (Figure 6) based on the tubulin cytoskeleton. The topology of the organelle system, as well as the modalities of their formation and management, make it possible to differentiate at least two large subnetworks.

Box 1. The eukaryotic cytoskeleton

The cytoskeleton allows the eukaryotic cell to retain its shape but also, due to its dynamics, to change shape and move around. It is also involved during cell division to separate genetic material and enable intracellular trafficking. It is made up of 3 types of elements:

1. Microfilaments produced by the polymerization of actin. A microfilament is about 8 nm in diameter. Actin is recruited from its monomeric form (G-actin) and is incorporated as F-actin. Actin is conserved in all eukaryotes and is used to (1) ensure the formation and transport of vesicles, (2) divide the cell into two daughter cells (the modalities of this role vary depending on the organism) and (3) generate pseudopodia for displacement.
2. The microtubules resulting from the polymerization of α-tubulin/β-tubulin dimers in the form of protofilaments, associating in groups of 13 to form tubes with a diameter of 24 nm. Like actin, microtubules are conserved in all eukaryotes and participate (1) in the transport of intracellular cargo, (2) ensure the division of chromosomes during mitosis and meiosis and (3) participate in the development of flagella that allow swimming.
3. Intermediate filaments which, unlike the previous ones, do not have the same composition in different groups of eukaryotes.

First, the nuclear envelope and the endoplasmic reticulum are in physical continuity. Vesicles transport components internal to the reticulum to the Golgi apparatus and then to the exocytosis pathway (Figure 4). Conversely, the endocytic vesicles converge towards the endosomal compartment. This is in relation with the Golgi apparatus, and the other organelles, always via diverse vesicles (Figure 4). Likewise, several organelles surrounded by a single membrane, such as peroxisomes or inclusion bodies, derive by modification from vesicles arising either directly from the reticulum or from other components such as endosomes or Golgi. Some of these organelles, such as peroxisomes, have specific functions of sequestering dangerous metabolites, and others, such as lipid inclusion bodies, of storing nutrients. This first network also contains the autophagosomes although these are delimited by two membranes. Indeed, they are formed by elongation of vacuoles around the cellular components to be degraded. This “nucleus/reticulum/golgi” network should be compared with the sterol content in eukaryotic membranes. Sterols confer special biophysical properties, in particular, they facilitate membrane fusions and modulate fluidity and stability. Its management is under the control of small proteins hydrolyzing GTP (G proteins of the Rab, Ran, Rho family, etc.). The formation and transport of vesicles is mainly dependent on actin, although microtubules may be involved in transport. It therefore seems that this network can derive by successive specializations from the same initial organelle.

Secondly, to this first network, we must add another one, formed by mitochondria whose genesis involves division from pre-existing mitochondria and which is not in connection via vesicles with the nucleus/reticulum/golgi network. The mitochondria has its own genome which participates, along with the nuclear genome, in mitochondrial biogenesis, which therefore takes place completely independent of vesicular transport. The mitochondria therefore form a second sub-network independent of that of the nucleus/reticulum/golgi. Finally, in algae and plants, there is an additional compartment with properties very similar to those of mitochondria: plastids, which like mitochondria have their own genome. These therefore form a third sub-network independent of the other two in photosynthetic eukaryotes, even if in some algae, it is embedded in the nucleus/reticulum/golgi network.

The presence of these organelles implies other functional consequences compared to prokaryotes. First, the presence of the nucleus allows additional steps in the regulation of gene expression. Indeed, the decoupling between transcription and translation as well as the splicing of the numerous introns allow the storage of the mRNA for later use, and to modulate not only the quantity of the mRNAs, but also their very nature thanks to alternative splicing. The nucleus contains most of the genetic material. It is probable that the sequestration of the genome in the nucleus made it possible to increase the cell size and therefore to make the eukaryotic cell even more complex, which in turn necessitated an increase in the complexity of the genome! Indeed, in eukaryotes, the size of the genomes varies from 2.2 Mb, a size smaller than certain bacterial genomes both in nucleotides and in number of genes, to the extraordinary one of 140,000 Mb, or 140,000,000,000 base pairs! Remember that the human genome contains about 3,000 Mb and codes for at least 25,000 genes and a large number of regulatory regions. Eukaryotic genomes are therefore often non-compact, with the presence of numerous introns, the combined size of which can sometimes exceed that of exons, and of selfish repeats such as transposons. Unlike prokaryotes, genes are not grouped into operons and polycistronic mRNAs are rare. However, in some groups of eukaryotes, genes can be co-transcribed and the pre-mRNA thus obtained is fragmented before translation. Finally, nuclear genetic material is present in the form of several linear chromosomes which adopt a very complex chromatin and supra-chromatin structure, in particular at the time of cell divisions. The processes of DNA partitioning are indeed much more complex than in prokaryotes. In general, division occurs by mitosis (Figure 7), and at the time of sexual reproduction in the form of meiosis (Figure 8). However, there are exceptions, for example in Ciliophora and Dinoflagellata which present amitotic-type partitions of nuclear material. The origin of mitosis and meiosis is still obscure. Indeed, if the genes involved in DNA replication and recombination (crossing-over) are present in prokaryotes, how did those involved in chromosome compaction, chromatid cohesion, microtubular network, cell fusion appear? Likewise, we do not clearly know the selection pressures that set up sexuality, because it does not have an immediate advantage, nor why some eukaryotes have lost it! Sexuality has three specific consequences, among other things. First, eukaryotes exhibit an alternation of haploid and diploid generations (Figure 9). As the genomes are different between haplophase and diplophase (see Box 2), alternation often makes it possible to express very different morphological and/or biological characteristics between haplophases and diplophases, ensuring a significant complexity of life cycles. In particular, the possibility of vegetatively growing via mitoses in each of the phases may vary depending on the species. Species with a majority haplophase are said to be haplobiontic (or haplophasic), those with a majority diplophase are called diplobiontic (or diplophasic), and those where the two phases have approximately equal durations haplo-diplobiontic (or haplo-diplophasic). Note that in Figure 9, plasmogamy and karyogamy, which are the two stages of fertilization, are dissociated. Indeed, there are organisms, like the Dikarya fungi, in which these steps can be separated by cell divisions that can occur for a very long time. During this dikaryotic phase, different characteristics of haplophase and diplophase may be expressed.

Plasmogamy can occur between identical or different gametes (Box 2). There are two types of incompatibilities between mutually non-exclusive gametes:

• Morphological incompatibility is often manifested by the need to merge a large, most often immobile, called female gamete, and a small, generally motile gamete, called male gamete. These gametes can be produced by two different individuals (called sexual) or by the same individual (called hermaphrodite). Rather, conjugation is called plasmogamy of two morphologically identical gametes, while fertilization is a more general term.
• Genetic incompatibility manifests itself in the impossibility for two genetically identical gametes to fuse; these can have different or identical morphologies. This situation can be found in different strains within the same species. Strains for which the gametes have no genetic incompatibility and which are therefore self-fertile are called homothallic, and those which, on the contrary, exhibit genetic incompatibility, thus being self-sterile, are referred to as heterothallic. In the latter case, mating types are defined. Individuals can only reproduce between compatible mating types. Most often there are two. This is called bipolarity and crosses are therefore possible between individuals of different mating types and impossible between individuals of the same type. Genetically, the mating type is dependent on a single locus with two idiomorphs. We speak rather of locus and idiomorph because often the genetic determinism is more complex than a gene with two alleles. In some species, the mating type is determined by two idiomorphs (tetrapolarity) having several alleles. Hundreds of combinations can be defined and the compatibilities between them are often complex with several thousand mating types! Sexual incompatibilities therefore increase the complexity of eukaryotic life cycles by introducing partners that are potentially different in terms of their morphology, their genetic characteristics or at both levels!

A second difference with prokaryotic cells, which allows the internal network of organelles to exist, is the possibility of compartmentalization of energy production by mitochondria and plastids and of enzymatic reactions between cytosol, peroxisomes, lysosome etc., as well as of storing energy reserves more effectively than in prokaryotes. Eukaryotic cells are therefore not optimized for immediate energy use, which probably allowed their complexification and participated in the emergence of multicellular organisms.

A final important characteristic of eukaryotic cells intimately linked to vesicular transport is that they have the possibility of endocytosis (Figure 10) and therefore of ingesting solid particles of large sizes. It is a fundamental property of eukaryotic cells that distinguishes them from prokaryotic cells. We will see that it is probably at the origin of their genesis and plays a very large part in their evolution because it allowed and still allows the entry of living organisms into the cell. If they are not digested, these can then behave like parasites, but can also establish more harmonious relations, persisting in the cell and giving it a selective advantage. We will see that sometimes, such endocytosis results can become integral parts of eukaryotic cells during long-term evolution.

Box 2. Ploidy levels

During their life cycle, eukaryotes have different genomes, which can have consequences on their phenotype. First, ploidy affects genome expression, and haploid and dikaryotic cells may not produce mRNA in the same proportion as diploid cells. One of the consequences is that diploid cells often are larger than haploid cells.

Second, diploid cells are the result of the fusion of two cells that can carry genetic differences. For example, in humans, haploid cells have either an X chromosome or a Y chromosome, while diploid cells are XX or XY. This last category, called heterozygous, clearly cannot be found in haploid cells! This case is general in heterothallic organisms which generally carry specific genes defining gender identity or species which have sex chromosomes that are responsible for morphological incompatibility during fertilization. The diploid is then heterozygous for the mating types or sex chromosomes while the haploids are homozygous.

Finally, in some eukaryotes, the nucleus can undergo changes in content or structure during the life cycle. Indeed, loss or amplification of DNA is observed in certain cells of multicellular organisms. Such cells are no longer intended to be used for reproduction (somatic cells) while germline cells intended for sexual reproduction retain all the genetic material. The most extraordinary case is that of the Ciliophora (Box 21), where expression is suppressed in one nucleus until the time of meiosis (called the germinal micro-nucleus) while cellular functioning is controlled by a giant nucleus (the macro- or somatic nucleus). The macro-nucleus derives from a micro-nucleus by amplification of certain regions of the genome and loss of other regions! Unlike the micronucleus, the macronucleus does not divide by classical mitosis but by nuclear fission. This case is not unique. It has been shown that in the yeast Schizosaccharomyces pombe, the microtubule spindle is not essential for division, in its absence the nucleus of this yeast divides according to a process of nuclear fission which could be the vestige of nuclear division before the invention of the microtubule spindle. Other types of non-canonical nuclear divisions exist, for example, in organisms lacking histone and whose genome does not compact in a classical way, such as Dinoflagellata (Box 23).

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