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Microbial Eukaryotes

Review of eukaryotic cell structure

• nuclear membrane - a double-layered membrane surrounding nucleoplasm. Nuclear pores control movement of large molecules in & out of the nucleus. The nuclear membrane physically separates transcription (in the nucleus) and translation (in the cytoplasm).
• endoplasmic reticulum & Golgi apparatus (also double layered). Internal membranes that are physically contiguous with the nuclear envelop. Used for the translation, processing, & export of lipids & secreted proteins.
• single-layer cytoplasmic membrane. Membrane lipids (all membranes) are predominantly glycerol phosphate esters of fatty acids. Also steroids, phytanyls.
• cell wall - carbohydrate (e.g. cellulose, chitin, chondroitin, etc)
• cytoskeleton - actin, tubulin, etc. Needed for transport of materials (organelles, chromosomes, etc) around in the cell, and also provide cell shape. Parts also form the spindle apparatus/centrioles and cilia/flagella.
• cilia & flagella are cytoplasmic extensions (not extracellular as in Bacteria & Archaea). Each has a basal body that is essentially a centriole.

Eukarya

Notice that there are no known primative branches and no known deep branches - there's a long unbranched 'trunk' on the tree before the first branch. Unlike in the Bacteria, the early branches (relative to abundant familiar organisms) are not primative. The familiar species are all relatively closely related on one small branch of the tree.

It should be said that the arrnagements of deep branches within the eukaryotes are very controversial. As more and more conplete genome sequences are determined, it is hoped that this tree will be better resolved.

The 'Archaezoans'

These are the anaerobic protists that diverged early from the other eukaryotes, either before the ancestor of those organisms aquired the mitochondrion (remember - by symbiosis), or alternatively they may have lost their mitochondria. The name is deceptive; they are not a single group, but many separate groups, and they are not primative; they are actually more derived than the plants, animals, and fungi, at least in terms of gene sequences. There are thousands of species of archaezoans, most of which have never been cultivated. The few that have been cultivated and studied are primarily the parasites, where there is incentive to tackle the hard work required.

Diplomonads - Giardia & relatives

These organisms are binucleated, flagellated anaerobes (no mitochondria). The well-studied species are gut symbionts that cause dysentery, but there are some free-living species. Division occurs by binary fission, creating 2 uninucleate daughter cells, which quickly undergo mitosis to regenerate the normal binucleate structure - mitosis is after division, not before.

They retain many primative traits that have been changed in the main branch of eukaryotes. For example, translation of mRNAs by their bacterial-sized (70S) ribosomes is initiated by Shine-Dalgarno-mediated interactions rather than by 5'-cap-binding and scanning. Because of this, genes are encoded in multicistronic operons, as in Bacteria & Archaea.

Microsporidians

Intracellular spore-forming parasites of animals (mostly insects). Very simple cellular structure, but this is probably due to simplification as part of their extreme parasitic lifestyle. They lack (in adition to mitochondria) Golgi, centrioles, flagella, and lysosomes.

Parabasalians

The known species in this group are common animal gut symbionts. A few are parasitic, such as Trichomonas, that causes PID in women. Barbulanympha predominate the gut of wood-eating insects, and are required for the ability of the insect to digest wood. The protist degrades the cellulose & metabolizes the resulting sugar to acetate anerobically, which is excreted and absorbed by the insect as it's primary nutrient.

Euglenozoans

These are the euglenoids, kinetoplastids, & amoebaflagellates. They have mitochondria and are typically flagellated.

Euglena is a common photosynthetic protist. It is flagellated (1 or 2 flagella), but also moves in a distinct 'inch-worm' manner and can usually also grow heterotrophically or phagotrophically. It used to be studied as a model for plant photosynthesis, but it is now known that it is not related at all to green plants - it aquired it's chloroplast independently of the other photosynthetic eukaryotes. In fact, it looks like the Euglena chloroplast is actually the remnant of a eukaryotic (algae) symbiont, not a cyanobacterium. But, it still serves as an example of why it's so important to know what your organisms is phylogenetically!

Trypanosomes are free-living or parasites with very complex life cycles. The free-living species are common soil organisms, but rarely cultivated. The parasites are well-studied because of the important diseases they cause, for example sleeping sickness & Chagas disease. They are actually very common arthropod gut symbionts.

Slime molds

The 2 types of slime molds, cellular and acellular, are actually 2 very different groups that are not at all related. Each is really a separate branch on the eukaryotic tree. Thy used to be thought of as fungii, but they are not at all related to them. They are amoeboid soil organisms.

Cellular slime molds
e.g. Dictyostellium, with a life cycle very much like the Myxobacteria.

Acellular slime molds

• Diploid phase - masses of cytoplasm with many nucleii but no membrane separating individual cells. Grow by just increasing in size & number of nucleii. Produce fruiting bodies & spores by meiosis, much like the cellular slime molds. Spores germinate into haploid individual cells.
• Haploid phase - individual cells, divide by fission, congugate (fuse) with other hapoid cells to produce diploid phase cell. This phase is usually transient, and they can be thought of a gametes.

Alveolates

These are the ciliates, dinoflagellates, and apicomplexans. They are a very diverse group of organisms, but all have vesicular membrane structures underneath their cell membrane, and are all related by ancestry. The apicomplexans are not well studied except Plasmodium, the causative agent of malaria, probably the single most important disease in man.

Ciliates

e.g. Paramecium. These are common, familiar organisms. Cilia are really just short, numerous flagella organized by a complex microtubule network just under the cytoplasmic membrane. Ciliates are very morphologically complex.

These organisms have 2 types of nucleii:

• macronucleus - active, vegitative nucleus, required for survival & fission. Polyploid (20-100n), with selective loss & amplification of various genes as needed, often with short pieces of DNA, even single genes, as individual chromosomes.
• micronucleus - dormant 'pristine' germ-line genome - required for sexual reproduction.

Most reproduce by fission most of the time, but periodically require sexual reproduction for viability - conjugation (exchange of a micronucleus) leads to recombination, then fission to re-sort genes.

Dinoflagellates

Usually photosynthetic flagellates - the 2 flagella are oriented at right angles, and they often have cellulose cell walls. Although most are photosynthetic and have chloroplasts, like the euglenoids they are not related to plants and often aquire their photosynthetic symbiontic cyanobacteria on an as-needed basis from their diet. They can sometimes keep the chloroplasts of eukaryotic algae from their diet - these are called "kleptochloroplasts".

They are quite versitile, and often have complex life cycles. They are common symbionts of animals, such as reef-building corals and marine clams. On the other hand, they are also the causitive agent of red tide and ciguatera poisoning. Pfisteria is notorious in North Carolina. Interestingly, these organisms generally lack histones and do not condense their chromosomes during mitosis or meiosis.

Heterokonts

This group contains the golden-brown algae (Crysophytes), diatoms, and brown algae.

The golden-brown algae and diatoms are specifically related. Diatoms are unicellular gliders; this gliding works via the same mechanism as in Bacteria, and the polysaccharride they secrete is the source of muscelage. These organisms have elaborate silica (glass) cell walls, and are most common in freshwater, but also exist in marine environments & soil.

Brown algae are usually filamentous, but some form quite large colonies, e.g. kelp and sarghassum (abundant seaweeds in this region). Unlike the diatoms, these have cellulose cell walls and are commonly found in marine environments.

Rhodophytes (red algae)

These are multicellular leafy organisms. They are predominantly marine, with cellulose cell walls. These are abundant reef-building algae, and some species produce large amounts of agar and carrageenan.

Chlorophytes (green algae & plants)

Most of these organisms are unicellular flagellates, e.g. Chlamydomonas, or filamentous (e.g. Spirogyra) - but vascular plants & bryophytes (mosses) are members of this evolutionary group. Energy & carbon are stored in the form of starch, and cells have cellulose walls, often with significant amounts of pectin &/or phenolics in the case of vascular plants & mosses. They are common in freshwater & terrestrial environments.

Fungi

All are non-photosynthetic (saprophytic). Most are filamentous (molds) or unicellular (yeasts) free-living microbes, but a few can produce macroscopic fruiting bodies, a.k.a. mushrooms. Most are soil organisms, some freshwater, and some are symbionts or parasites of plants & animals. They have chitin and/or cellulose cell walls.

Choanoflagellates & animals

Choanoflagellates are small, marine non-photosynthetic (phagotrophic) protists that feed by beating a single flagellum to produce a flow of water, from which they trap bacteria with tenticle-like cilia. They often have intricate external structures called 'lorica', and resemble the individual cells of sponges. These organisms probably resemble the ancestral protists from which animals arose.

Animals are colonial or multicellular organisms with chondroitin cell walls. All of the main groups (phyla) of animals arose more-or-less simultaneously in the 'Cambrian explosion'. Morphological classification is fairly consistant with the molecular phylogenetic data - probably because of their morphological complexity.

Most of the animals are microscopic. The most abundant groups by far are microscopic nemotodes and arthropods.

Eukaryotic evolution

Eukarya are morphologically complex, but biochemically simple compared to either Bacteria or Archaea. Eukaryal evolution is predominated by increased genetic complexity. This genetic complexity may have been made possible by the invention of the cytoskeleton, which allows more complex cellular organization and more complex genetic organization via mitosis & meiosis.

Symbiosis has played an important role in eukaryotic evolution. Primordial eukaryotes were prokaryotic and may have been fairly similar to the Archaea, to which they are related. Nearly all eukaryotes have an actin/tubulin cytoskeleton and a set of related membranous structures: the nuclear envelop, endoplasmic reticulum, Golgi, lysosome, and transport vesicles. These must therefore have been acquired early in the evolution of eukaryotes.

Later, perhaps (or perhaps not) after the divergences that create the various groups of archaeozoans, the ancestor of the rest of the eukaryotes formed an endosymbiotic association with an aerobic alpha-purple bacterium. This association became permanent - neither symbiont can now (usually) survive without the other. The bacterial symbiont evolved dramatically, and most of it's genes have been transfered to the nuclear genome - we call them mitochondria. However, it may also be that these organisms diverged after the aquisition of the mitochondrion, and has subsequently lost then by evolutionary simplification - evidence for this is the presence of bacterial-type genes in their nuclear genome that may have come from the mitochondrion prior to it's loss.

The similar acquisition of chloroplasts by symbiosis of a eukaryote with a cyanobacterium (or in a few cases with eukaryotic algae) occured several times - probably each of the major groups discussed above aquired their plastids independently. Plastids were apparently never aquired by archaeozoans, nor are they known to form other types of symbioses with cyanobacteria - after all, cyanobacteria produce oxygen, which is toxic to eukaryotes without mitochondria!

Some believe that the aquisition of the centriole/cytoskeleton/spindle/flagella was also a symbiotic event - a fusion of a nucleated organism with a spirochate or some now extinct group of organisms. But, there is no DNA associated with these organelles, & the genes that encode their components are typical eukaryal genes, so there is no molecular data to support this. On the other hand, the centriole (the basis for all of the others) is replicated by division and cannot be regenerated from scratch in the cell - like the mitochondria & chloroplasts!

Questions for thought

• Think about all the ways in which gene expression is different in Bacteria and plants/animals/fungi. How do you think these processes work in more deeply diverging eukaryotes? Why do you think this?
  
  
• There has been a lot of uncertaintly about whether "algae" represent a single group that acquired chloroplasts (cyanobacteria) once, or whether chloroplasts were acquired by several eukaryotes, each being the origin of one kind of algae. How would you answer this question? What would be the problems with your approach?
  
  
• Some evolutionary biologists believe that archaeozoans never had mitochondria - that is, that they diverged from the other eukaryotes before thy acquired them by symbiosis. Many others believe that this symbiosis predates the last common ancestor of eukaryotes, and that the "archaeozoans" (a term they consider a misnomer) have lost mitochondria. What approaches can you think of that might be used to resolve this issue?
  
  
• Some unicellular eukaryotes that lack functional mitochondria have other organelles that provide them with better sources of energy metabolism than substrate-level phosphorylation. An example of this are the hydrogenosomes of archaeozoans, anaerobic ciliates, and even some fungi. These organelles lack DNA. How might you try to determine the origin of these organelles, and whether they are related to each other (not just labeled the same), and whether or not they are descended from mitochondria?

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