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THE EUKARYOTIC NUCLEUS

    How many types of cell are there?  Until  recently, it seemed that there were two kinds of cell: prokaryotic and eukaryotic.  Bacterial cells are prokaryotic: they are smaller and lack a nucleus (and other internal membrane-bound organelles).   The eukaryotic cells are larger and more complex, composing the cells of animals, plants, and fungi in addition to the protists (algae, amoebae, and others).  It was simply assumed that all cells which were not eukaryotes were similar and should be grouped together as prokaryotes.  We now know that there are two groups of prokaryotes which are as distinct from each other as they are from eukaryotic cells (Lopez-Garcia, 1999).  The newly discovered group is known as the archebacteria, or archaea. 

Archebacteria

archebacteria archebacteria
Eubacteria:
eubacteria eubacteria
eubacteria

WHICH 2 OF THE 3 DOMAINS OF LIVING THINGS ARE MOST CLOSELY RELATED?

     If there are three groups of living things, one would predict that two of them shared a common ancestor more recently than with the third.  Molecular comparisons should indicate which of these two groups are most closely related.  Some evidence could be used to indicate a close relationship between eubacteria and archaea in addition to their prokaryotic cell structure.  There are cellular processes which are shared between archaea and eubacteria including glycolysis, polysaccharide metabolism, sulfur oxidation and reduction, nitrogen fixation, cell cycle regulation, and flagellar motion (Woese, 1998). Archebacteria have an operon-like organization of genes, similar to eubacteria (in both operon organization and the order of genes in the operons). (Gray, 1992).  Eukaryotes use a broader range of functional RNA molecules than do bacteria.  This could be the result of the eukaryotic lineage retaining more vestiges from the RNA world which were replaced by protein in prokaryotic lineages (Hartman, 1984).

     In other ways, however, archaea are unlike both eubacteria and eukaryotes.  A diversity of archaeal cell wall and cell membrane materials are known, suggesting that the archaeal lineages diverged from each other before a common structure was established.  The early archaea probably lacked a cell wall.  The cell membrane in archaea is composed of L-glycerol phytanylether lipids as opposed to the D-glycerol acylester lipids in eubacteria and eukaryotes (Kandler, 1994).   The uniqueness of archebacteria, in some characteristics at least, may be the result of archaea having changed the least from the ancestral progenote condition (Gray, 1992).  Genetic comparisons indicate that gram positive eubacteria are more closely related to archaea that gram negative eubacteria.  Deinococcus and Thermus seem to be intermediate between gram positive and gram negative bacteria (Gupta, 1998).

     There are a number of features which were once thought to distinguish eukaryotes and prokaryotes which are now known to be shared between archaea and eukaryotes, suggesting that archaea are more closely related to eukaryotes than are eubacteria.  For example, archaea transcribe DNA through mechanisms which were formerly considered to be eukaryotic.  In eukaryotes, transcription factors are required to begin transcription while in eubacteria, RNA polymerase can bind DNA strands without them.  Archebacteria seem to require transcription factors for transcription, suggesting links to eukaryotic mechanisms (Ouzonunis, 1992).  Archaea possess a promoter sequence similar to the TATA box of eukaryotes, genes homologous to the TBP transcription factor in eukaryotes, and a homolog of the eukaryotic translation elongation factor TFIIS (Langer, 1995; Thomas, 2001).  Archebacteria and eukaryotes both utilize the general transcription factor  TFIIB (Bagby, 1995).   While the large subunits of RNA polymerase are homologous in all three domains of life, archaea are more like eukaryotes in their promoter sequence for RNA polymerase II promoters (TATA box) (Langer, 1995). 

     Archaea possess histones and form nucleosomes homologous to those of eukaryotes (Lopez-Garcia, 1999).  Archaea resemble eukaryotes more than eubacteria in their polymerase, DNA replication factors, DNA repair enzymes, cell division control proteins, proteasomes, protein transport systems, elongation factors EF-1α and EF-2, α and β subunits of ATPase.  Archeal mechanisms in translation (5S rRNA, initiator tRNAmet, and promoter sequences) are more similar with those of eukaryotes.  There are several ribosomal proteins shared between archebacteria and eukaryotes which are not known from eubacteria.  Six of the archaeal subunits of RNA polymerase are only known in eukaryotes.  Primer recognition and the use of 7S RNA is also more similar to eukaryotes. Examples of a molecular chaperone protein (similar to a eukaryotic mitotic spindle protein), the use of the amino acid hypusine (previously known only from eukaryotes), and eukaryotic-like sensitivities to toxins and antibiotics are known in archebacteria. The archaea known as Crenarchaeota are thought to be most similar to the ancestral archaeon and also seem to be the most similar to eukaryotes.  (Gray, 1992; Olsen, 1997; Bult, 1996).

     Sequence comparisons of many genes supports that archaea are more closely related to eukaryotes than either are to eubacteria.  A grouping of the eukaryotes with archaea is supported with adenylosuccinate synthase, arginosuccinate lyase, aspartate aminotransferase, deoxyribodipyrimidine photolyase, dihydroorotate oxidase, ferredoxin, glutamate dehydrogenase, glutamine synthetase, glycine hydroxymethyltransferase, lactate dehydrogenase, pyrroline -5-carboxylate reductase, pyruvate kinase, ribose-phosphate pyrophosphokinase, thronyl tRNA synthetase, triose-phosphate isomerase, UDP glucose epimerase, and valyl-tRNA synthetase (Katz, 1998). 

     All of this evidence seems to suggest that archaea are more closely related to eukaryotes.  However, there is evidence which suggests the contrary.  Sequence comparisons of many genes supports that eubacteria are more closely related to eukaryotes than either are to archaea.  These genes include arginosuccinate synthase, aspartate transcabamoylase, aspartyl tRNA synthetase, ATP synthase alpha chain, ATP synthase beta chain, DNA dependent RNA polymerase, DNA polymerase II elongation factor Tu, elongation factor 2, histidyl-tRNA synthetase, hydroxymethylglutaryl CoA reductase, indole 3 glycerol phosphate, isocitrate dehydrogenase, isoleucyl tRNA synthetase, ribosomal proteins, RNA polymerase subunit A, RNA polymerase subunit B, tryptohanyl tRNA synthetase, tyrosyl-tRNA synthetase (Katz, 1998)

 

     What conclusion should be drawn from data which conflicts?  There is data which supports each of the two phylogenetic trees depicted below.

trees

There is conflicting evidence regarding the question of the relationships between these three domains of life.  Another unanswered question is the origin of the eukaryotic nucleus.  In now seems that these two questions are related and the answer to each of them may be the same.

THE EVOLUTION OF THE EUKARYOTIC NUCLEUS

Eukaryotic innovations include the cell cycle complete with a chromosome segregation apparatus, sexual reproduction complete with recombination, a cyctoskeleton, spliceosomes and introns, small regulatory RNAs, vesicular transport based on membrane proteins, serine/threonine/tyrosine kinase signaling networks, the use of ubiquitin in post-translational protein modification, and a variety of new genes (Aravind, 2006).

 

    Eukaryotic cells possess a very prominent nucleus which contains the chromosomes, as evident in the human neuron and oocyte below.

neuron

 

     The nuclei of the human cells of the preceding images store 46 chromosomes, which serve as the genetic blueprint to synthesize all the proteins and RNA molecules human cells will need.  Human chromosomes are pictured below.

chromosomes
     How did the eukaryotic nucleus evolve?  It may be that prokaryotic cells simply produced additional membrane which surrounded the bacterial chromosome.  This is apparently possible since the DNA of the eubacterium Gemmata obscuriglobus is enclosed by two membranes.  It is not known whether this membrane will provide insight into the evolution of the eukaryotic nucleus and there is no evidence of nuclear pores or of a nucleolus (Fuerst, 1991). Other proteobacteria also have been found with membrane-bounded chromosomes (Margulis, 2006).If the eukaryotic nucleus evolved this way, one would expect one of the two types of prokaryotes to be more closely related to eukaryotes.
endosymbiosis

There are other possibilities which are more complex.  It is possible that some type of fusion occurred between the cells.

endosymbiosis

     There is a great deal of evidence that supports the theory that mitochondria and chloroplasts are actually the descendents of eubacteria that were engulfed by a proto-eukaryotic cell and survived as endosymbionts (cells living inside other cells).  This question is addressed in the next chapter.  It is possible that the eukaryotic nucleus also resulted from an endosymbiotic event.  In such a model, an archaeal cell could have engulfed a eubacterial cell.  The origin of the eukaryotic nucleus by endosymbiosis was first suggested in 1910 (Hartman, 2002).

    The nucleus is surrounded by a double-membrane, just like all other known endosymbionts.  One of the membranes originated from the cell membrane of the endosymbiont while the other originated in the host vesicle which enclosed it (Hartman, 1984; Hartman, 2002).  The eukaryotic nucleus could have evolved from the fusion of a thermoacidophil archebacterium fused with a motile eubacterium.  The resulting eukaryote would have inherited much of its translational machinery from the archebacterium and its microtubule organizing centers, heat shock proteins, and other proteins from the eubacterium.  This would neatly explain why some molecular comparisons suggest a close relationship between eukaryotes and  eubacteria, while other molecules suggest a close relationship between eukaryotes and archaea (Margulis, 2000).

     Although some feel that the eukaryotic cell formed when an archaeal cell engulfed a eubacterium, the major problem with this model is that no known modern bacteria possesses a flexible cytoskeleton which interacts with the cell membrane to permit phagocytosis.   One model of the origin of the eukaryotic cell is that an RNA based organism (termed a kronocyte) engulfed a prokaryote which eventually became the nucleus.   Indirect evidence of the existence of this third type of cell, the proto-eukaryotic kronocyte is found in the cellular features of eukaryotes which are unique and are not found in either archaea or eubacteria. 

The proteins unique to eukaryotes include cytoskeletal proteins (tubulins, actin, tubulin-associated proteins, and actin associated proteins) and proteins associated with endocytosis (clathrin, clathrin associated proteins, and dynamin).  Other proteins unique to eukaryotes include ribosomal proteins, proteins of the ER and Golgi, signaling molecules, ubiquitin, ubiquitin-like proteins, ubiquitin protease, ubiquitin conjugation enzymes, 14-3-3 proteins; B cyclin, some regulators of cell cycle, introns and gene promoters (Hartman, 2002; Xu, 2002; Katz, 1998). 

     In this model, a phagocytic kronocyte engulfed an archaea and the plasma membrane of the archaea formed the nuclear membrane.  The genetic fusions which gave rise to the nucleus and mitochondria seem to have been separate given the differences between nuclear and mitochondrial homologs of the certain proteins (Gupta, 1998).  The resulting cell would have possessed many nuclear genes having been derived from the archaeal chromosome, some resulting from the transfer of mitochondrial (eubacterial) genes to the nucleus, and some from the original kronocyte.

endosymbiosis

     Comparisons of gene sequences indicate that eukaryotes resulted from a combination of genomes most similar to those of thermoacidophilic archaebacteria and gram negative eubacteria.  Most genes involving the processes of information transfer in eukaryotic cells seem to have derived from archaea.   A number of eukaryotic genes are known in eubacteria but not in archaebacteria.

 

    If the above model were true, it would be difficult to trace the ancestor of eukaryotes since a number of distinct organisms contributed genes to the resulting cell.  Since there is ample evidence of genes being transferred to the nucleus from organelles in modern endosymbionts, it is difficult to identify the origin of modern genes located in the nucleus.  Another complicating factor is that lateral transfer continues to occur today in which a cell can absorb DNA from its environment and incorporate it into the genome.  The human genome possesses a number of genes which seem to be of bacterial and viral origin through lateral transfer.       Some have even suggested that viruses predate eukaryotic cells and that a virus might have been involved in the origin of the nucleus. (Forterre, 2002).  The fact that viruses encode proteins not known to have any cellular homologs may support the hypothesis that they are descended from an early form of life which was outcompeted by the ancestor of modern living organisms and could only survive by parasitizing cells (Forterre, 2005).

VIRUSES

     Could viruses have been involved in origin of the eukaryotic nucleus?  Many scientists feel that viruses are forms of life which are remnants of very early, primitive organisms. Viruses are much more abundant than are often assumed.  A milliliter of seawater usually contains about 10 million viral particles.  The sum total of carbon tied up in marine viruses may be 270 million metric tons, which is 20 times greater than that contained in the sum of all whales (Balter, 2000). The number of viruses estimated on earth today is 10 (exponent 31) to 10 (exponent 32) , which is at least ten times the number of estimated cells on earth (Bamford, 2005). The most abundant viral classes are those which infect bacteria (Bamford, 2005).

The eukaryotic nucleus shares some characteristics with some viruses.  Both viral genomic mechanisms and the eukaryotic nucleus separate transcription from translation, cap their mRNAs, and possess linear chromosomes.  Some viruses, such as poxviruses, possess α-polymerase enzymes similar to those of eukaryotes.  Some have suggested that the eukaryotic nucleus originated with the endocytosis of a complex DNA virus (Bell, 2001; Takemura, 2001). Double stranded DNA may have originated as a viral strategy to defend against cellular defense mechanisms which silenced single stranded viral RNA (Lupi, 2007).

Among the RNA viruses, Nidovirales possess the largest genomes or up to 32 kb (more than double that of related RNA viruses) (Gorbalenya, 2006). There is a family of large DNA viruses known as the nucleo-cytoplasmic large viruses (NCLDV). The ancestral member possessed at least 41 genes and some members of the family have grown considerably through horizontal transfer. Because they encode their own replication and transcription proteins, they are less dependent on their cellular hosts than other viruses (Lakshminarayan, 2006). The family of nucleocytoplasmic large DNA viruses (NCLDV) seem to have descended from a common ancestor and infect diverse organisms such as animals, algae, and protists. Many of their genes originated from bacterial hosts (Filee, 2007). The genome size of the mimivirus consists of 1.2 Mb of linear double stranded DNA. This is larger than that of the intracellular parasitic bacteria U. urealyticum and about the same size as those of other intracellular parasitic bacteria. The mimivirus is similar in size (0.4 microns) to small bacteria and possesses more than twice the number of genes as the smallest parasitic bacteria. About 91% of its genome is coding and includes the sequences for more than 900 proteins, such as DNA polymerase, transcription factors, and DNA repair proteins (Suzan-Monti, 2006).

DNA viruses other than the Mimivirus do not possess conserved promoter sequences to signal the start points of their genes. About half of the Mimivirus genes possess an upstream element AAAATTTGA. This unique conservation and its similarity to the core promoter element TATA in eukaryotes supports the hypothesis that an engulfed virus might have been converted into the eukaryotic nucleus (Suhre, 2005).

Double-stranded DNA viruses infecting archebacteria and isolated from hydrothermal vents replicate their DNA in a manner similar to the large dsDNA eukaryotic viruses. Environments in the vicinity of geothermal heat typically a much greater diversity of viruses than more typical aquatic environments. The ends of the linear chromosomes are replicated by a mechanism which resembles that of telomeres, supporting the hypothesis that eukaryotic nucleus arose from viral precursors (Prangishvili, 2004).

How did viruses evolve? Three possibilities have been suggested for the origin of viruses: that they are remnants of entities that evolved prior to cells, that they are the descendants of unicellular organisms that have been reduced to an extreme degree as an adaptation for parasitism, and they arose from genetic material from cells which could propagate itself. Although some have suggested that the ancestors of cells were virus-like entities which used the primordial soup as a host, this is not widely accepted. There is no evidence to indicate that viruses are derived from modern cells although the ancestors of modern cells might have been simpler and thus more likely candidates for the ancestors of viruses (Forterre, 2006).

There are several lines of evidence which indicate that groups of viruses are both related and ancient such as similarities in structure, molecular similarities (such as the structure of DNA polymerases), life cycle similarities, and the adaptation of group members to bacteria and eukaryotes. DNA viruses might have evolved from RNA viruses and the diversity of DNA replication proteins which are unique to viruses suggests that the transition from RNA to DNA may have occurred first in viruses. Viral proteins may have been co-opted into the ancestors of cells to permit the transition from RNA to DNA. Genetic comparisons of homologous proteins involved in DNA function from eukaryotes, bacteria, and viruses support this possibility (Forterre, 2006). Molecular similarities suggest that viruses infecting bacteria and those infecting animals are descended from a common, ancient ancestor (Benson, 2004). Some have proposed that the self-assembly mechanisms of viral capsid proteins and the self-propagation of prion proteins are vestiges retained from the earliest cells (Lupi, 2007).

Plasmids possess genes unrelated to those of the host but which seem to be derived from a viral origin (Forterre, 2006).

BASAL BODIES, CENTRIOLES, CILIA, AND FLAGELLA

BASAL BODIES AND CENTRIOLES

Basal bodies are similar to centrosomes, being composed of centrioles and surrounding pericentriolar elements (Fliegauf, 2006). Proteins such as CP110 and CEP97 help determine whether a centriole becomes a basal body (Bettencourt-Dias, 2008). While most cilia are assembled from the basal body after it has docked with the plasma membrane, the axoneme can be synthesized in the cytoplasm (such as in the sperm of flies) (Fliegauf, 2006). The basal body of the primary cilium is developed from the mature centrosome of mother/daughter centrosome pair (Whitfield, 2007). Sperm contribute basal bodies to ova whose centrioles were lost during oogenesis (Bettencourt-Dias, 2008).

The mitotic spindle can form without a centrosome. The lack of a centrosome does inhibit the formation of the aster and increase the frequency of irregular cytokinesis, but cytokinesis can also occur without centrosomes. The only processes which cannot occur at all without centrosomes are the formation of flagella and primary cilia (the latter of which are required for development). Progression through G1 also can depend on centrosomes in a way independent of the role in organizing the spindle (Reider, 2001). There are some cases in which centrioles can be generated without pre-existing centrosomes. While centrosomes are essential for the survival of an organism, stable animal cell lines can be established without centrosomes. Many cells from flies to fish to mammalian kidney cells can produce normal mitochondrial apparatuses without centrosomes (Reider, 2001; Beisson, 2003).

Centrosomes can function in the establishment of polarity within a cell. This may represent a primitive function which led to the establishement of a basal body at the cell membrane for polarity (Mitchell, 2004).

CILIA

Cilia and flagella were among the first organelles found in eukaryotes; the last common ancestor of all modern eukaryotes possessed a nucleus, mitochondria, and flagella/cilia (Mitchell, 2004). Cilia are present in most protists. A number of specific cell types in invertebrates express cilia such as sensory neurons in nematodes and flies (where they are present on dendritic ends) or sperm in flies. In contrast, they are widely present on the cells of eukaryotes where they have been modified for a great diversity of functions ( Davis, 2006).

Cilia are only 0.2-0.3 microns wide but can extend for 3 to 30 microns from the cell surface. Although cilia are not surrounded by a membrane, the basal body separates them from the remainder of the cytoplasm. From the basal body, microtubule triplets extend into the cytoplasm and into the transition zone at the base of the cilium ( Davis, 2006).

Bending of cilia opens calcium channels (made of PC1 and PC2). The most common form of ciliary movement involves central pair of microtubules and their dynein links to the other doublets ( Davis, 2006). The central pair of microtubules is important for motion and, although motility may not have been the original function of proto-cilia, this mechanism was established by the last ancestor of modern eukaryotes (Mitchell, 2004). Cilia can bend in three separate ways: a sine-like wave motion, a broad stroke motion, and twisting along its axis (the latter of which occurs at the embryonic node). The ciliary membrane is also capable of transporting substances along its surface or allowing a unicellular eukaryote to glide along a surface through an unknown mechanism that may involve the IFT. This gliding mechanism is observed both in primitive eukaryotes and mammalian cells. It is thought that this gliding mechanism may represent the original contribution of cilia to motility in ancestral cells ( Marshall, 2006).

The shaft of the cilia or axoneme is composed of 9 pairs of microtubules (A and B tubules) which may surround a central pair of tubules (Fliegauf, 2006). Given the occurrence of the 9+2 microtubule arrangement in diverse eukaryotic cilia, it is thought that this represents the ancestral organization of the structure. Modern organisms have developed a number of modifications to the ancestral 9+2 arrangement such as the 9+0 arrangement common in vertebrate nonmotile cilia, or the rare14+0, 12+0, 9+0, 6+0, or 3+0 organizations in motile cilia (Mitchell, 2004).

Cilia with 9+0 microtubules are usually nonmotile (although diatom and eel gametes or embryonic cells in mice and zebrafish are exceptions). While most 9+2 cilia are motile (such as those lining respiratory passageways or on ependymal cells), others are nonmotile (such as those of the ear). While most 9+0 cilia are nonmotile (such as those of photoreceptors and renal monocilia), some are motile (such as the monocilia of the embryonic node). Elongated cilia in sperm and some protists are referred to as flagella. All types of cilia can potentially function in sensation (Fliegauf, 2006).

INTRAFLAGELLAR TRANSPORT

Since no proteins are synthesized inside the cilium, many must be transported through intraflagellar transport (IFT) mechanisms.IFT continues even after a cilium is full grown and cilia can be disassembled through IFT (Snell, 2004). Homologous IFT mechanisms which transport materials between the cell membrane and axoneme exist in diverse eukaryotes, including Giarda. Although Giardia posssess an IFT system, the basal bodies are located in the cytoplasm, far from the membrane. This may represent an intermediate stage in the evolution of an IFT system to synthesize cilia and flagella. There are a few examples of modern eukaryotes which can synthesize flagella in the cytoplasm and which lack IFT components (Briggs, 2004). The cell membrane around the axoneme includes receptors and channels. The matrix between the membrane and microtubules has the IFT machinery ( Marshall, 2006).

IFT utilizes kinesin-2 proteins for anterograde transport and dynein proteins for retrograde transport. Kinesin anterograde transport is required for the assembly of the cilium. Proteins required for IFT (such as Kif17/OSM-3) are conserved in animals as diverse as mammals and nematodes ( Davis, 2006). IFT mechanisms utilize homologs of proteins which regulate the mitotic spindle (Snell, 2004).

The dyneins and kinesins which are required for flagellar/ciliar function probably had roles in the microtubule movements in mitosis prior to the evolution of flagella (Mitchell, 2004). A number of proteins involved in flagellar transport also function in control of the cell cycle (Qin, 2007). Some have proposed that the original function of the centrosome was its role in cilia formation (Mignot, 1996).

FUNCTIONS OF CILIA

The number of roles known for modified cilia is expanding. The majority of mammalian cells form a single cilium (the primary cilium) which may function in signaling. In the brain, these primary cilia may express receptors for somatostatin and serotonin (Snell, 2004). The cilia of ependymal cells are required for normal migration of neuroblasts. Mutations affecting the monocilia (channel proteins PC1 and PC2) which extend from epithelial cells into kidney tubules cause polycystic kidney disease in mice and humans. A number of organs which enclose fluid can suffer defects in mice with mutations in ciliary proteins (including the cardiovascular system, liver, and pancreas) ( Davis , 2006). Monocilia expressed in the embryonic node are required for the acquisition of left/right asymmetry in the embryo. Mutations of proteins such as dyneins Ird and Dnahc5 can result in a randomized asymmetry ( Davis , 2006). Renal monocilia are sensory (Fliegauf, 2006). Primary cilia are longer near brain’s ventricles (Fuchs, 2004). Olfactory neurons and taste buds utilize their cilia to perceive smell and taste (Mitchell, 2004). Specialized cilia compose vertebrate photoreceptors and some mechano and chemical sensors in invertebrates (Avidor-Reiss, 2004). In the regulation of bone strength and structure, osteoblasts, osteocytes, and chondrocytes utilize their primary cilia to respond to compression and fluid movement in the canaliculi (Whitfield, 2007). Receptors on the cilia include EGF, serotonin, somatostatin, FGF, smoothened-patched (hedgehog), and PDGF receptors (Whitfield, 2007). The signals known to intact cilia and functioning ciliary proteins include hedgehog, Wnt/wingless, and PDGF ( Davis, 2006).One advantage to the use of cilia in sensation is that its great surface area to volume ratio allows second messenger molecules to accumulate to a high concentration ( Marshall, 2006).

The human diseases resulting from mutant genes affecting ciliary function include ciliary dyskinesia, polycystic kidney disease, male sterility, retinitis pigmentosa, Bardet–Biedl syndrome, and hydrocephalus (Fliegauf, 2006). Patients with ciliary disorders are also at increased risk for obesity, hypertension, diabetes, hearing disorders, anosmia, and developmental problems (Inglis, 2006; Snell, 2004).

PRIMITIVE EUKARYOTES

     There are a few types of primitive eukaryotes which lack mitochondria.  Although it was originally hypothesized that their lineages might have evolved prior to the acquisition of endosymbionts in ancestral eukaryotes, it now appears that these lineages once possessed mitochondria which were subsequently lost, given nuclear genes which seem to have originated in mitochondrial endosymbionts.  As a result, all known lineages of eukaryotes seem to have arisen after mitochondria were acquired in ancestral eukaryotes.  (One group which was once thought represent primitive eukaryotes, the Microsporidia, are now classified as modified fungi) (Keeling, 1998; Roger, 1999).

     Giardia, which lacks mitochondria, may be a member of the most primitive surviving eukaryote lineage, according to phylogenetic trees of some of the most conserved moelcules, such as HSP70 and 16S rRNA.   Giardia possesses 2 homologs of HSP70, one of which associated with endoplasmic reticulum suggesting that ER were present in the early eukaryotes (Gupta, 1994).

Given that giardia possess flagella, the cilia/flagella organelle evolved prior to the last common ancestor of the eukaryotes (probably in the form of a single flagellum). A number of cytoskeletal proteins unique to Giardia known as giardins have been identified. Many are homologs of the gene family of annexins in other eukaryotes. Given that several actin-associated proteins have yet to be found in Giardia and may be absent (such as tropomyosin), it could be that these proteins represent an alternate cytoskeletal organization from an early eukaryotic lineage (Weiland, 2005). Some of the most primitive eukaryotic lineages lack Golgi (although they may possess some of the components). Some have proposed that these lineages predate the origin of Golgi while others have proposed feel that the Golgi have been reduced in these lineages (Dacks, 2001). Giardia possesses 5 chromosomes and few introns (Weiland, 2005).

giardia

Giardia possesses genes for meiosis and there is some evidence of sexual reproduction although it is primarily asexual (Logsdon, 2008).

In dinoflagellates, microtubules are involved in mitosis (as in other eukaryotes) but the chromosomes are attached to the nuclear membrane and chromosome movement is caused by the membrane (as in bacteria).  This might represent an intermediate stage of chromosome separation from early in the history of eukaryotes.

 PHAGOCYTOSIS

Deoxyribonuclease II (DNase II) is a lysosomal enzyme found only in eukaryotes (and one bacterium, perhaps resulting from horizontal transfer). Its origin may be tied to the evolution of phagocytosis in basal eukaryotes (Shpak, 2008). In mice, mutations in DNaseII are life threatening (due in part to a reduced ability to digest nuclei by white blood cells) and in humans mutations have been linked to lupus erythematosus (Shpak, 2008).