Small Things Considered

Fine Reading: Two Fine Protist Blogs

by Elio

Merry and I would like you to know about two specialized blogs that deal mainly with protists, one called Skeptic Wonder, the other The Ocelloid. The first one is a spirited blog whose history goes back to 2008, the second a recent addition to the Scientific American Blog Network. Both are written by a friend and avid protistologist who goes by the name of Psi Wavefunction, and we’re glad to help publicize them.

We applaud the blogger's effort, in good part because we believe that protists need good press. Everyone has heard of them, perhaps encountering them as pond-scum paramecia in high school, when learning about malaria, or more recently in the hoopla about using micro-algae to produce fuels. But they deserve more attention than that for their enormous variety in shape, size, and genomic complexity. They have a central role in this planet’s metabolism, being responsible for a huge amount of carbon cycling. In addition, many, like the diatoms, are a joy to the eye.

The first issue of The Ocelloid is A Quick Dive into the Protist World, and quite a trip it is. Here you'll encounter organisms you may have heard about, or not—intricate radiolaria, filose amoebas that leave tracks on the sand, and gorgeous foraminifera. The name of this blog refers to an eye-like structures of dinoflagellates, the ocelloid. This is a true model biological wonder, with a complexity that approaches that of the vertebrate eye, all in one unicellular organism.

Many blogs deserve your attention, but these two stand out in our opinion.

 

Hard Biology

Pleurosigma (a marine diatom). Credit: Michael
Stringer, Westcliff-on-Sea, Essex, UK. Source.

by Elio

For some time, I've had the urge to learn something about diatoms. They are dazzlingly beautiful, relatively easy to manipulate, and have left a fossil record immense in quantity. I never had followed up on this yen, so here’s my chance. A recent paper shed light on the way they make their hard shells.

Diatoms are busy creatures, accounting by their photosynthesis for about 20% of the global primary production of organic material, an amount comparable to that produced by the tropical rain forests. They are single cells contained within a shell made up of glass (silica), which is what gives many of them often stunning shapes. Silica does not readily decompose and fossil diatom shells accumulate in prodigious quantities. Such deposits can be hundreds of meters deep in some places (fossils by the truckload!). Diatomaceous earth, as the rock consisting of fossil diatoms is called, has a large number of industrial uses, such as filtering pool water, absorbing oil spills, as a mechanical insecticide, as a mild abrasive (it may well be in your toothpaste!), and even as a component of dynamite! And, as we will see below, diatoms also have novel and unexpected uses.

Targeting an Achilles' Heel of Plasmodium

by S. Marvin Friedman

SEM of female Anopheles mosquito. Source.

Plasmodium falciparum accounts for 85% of all cases of malaria, and thus is the most deadly of the many species in this genus. About 250 million people are infected annually, of which about one million die. Of these deaths, 90% occur south of the Sahara desert in Africa, and most of the victims are children under the age of five. Malaria also occurs in southern Asia, Central and South America, the Caribbean, and the Middle East. Plasmodium, an apicomplexan protozoan, is also famous for its complex life cycle, some stages of which take place while within females of certain species of Anopheles mosquitoes, others while resident in the liver and red blood cells of humans who were bitten by these mosquitoes. The huge health problem of malaria is exacerbated by the alarming ability of this protozoan to rapidly develop resistance to chemotherapeutic agents. Thus, new antimalarials are desperately needed to bring this deadly disease under control.

In order to identify new drug targets, Istvan and coworkers analyzed P. falciparum mutants resistant to two commonly used antimalarials: thioisoleucine (an analog of isoleucine) and mupirocin (an antibacterial agent used clinically to treat MRSA infections). These two drugs kill blood stage parasites at micromolar and mid-nanomolar concentrations, respectively. For both drugs, increasing the isoleucine concentration in the medium increases the IC50 values (i.e., reduces killing efficiency), suggesting a competitive interaction between isoleucine and both drugs. The kinetics of killing are dissimilar for these two compounds, indicating that they inhibit different isoleucine utilization targets. These results are not surprising since, upon entering red blood cells (“ring stage”), the parasites degrade hemoglobin to obtain a supply of amino acids necessary for replication. Such scavenging is essential because the parasites lack most amino acid biosynthetic pathways. But isoleucine is the only amino acid absent from adult human hemoglobin, hence is the only one that must be obtained from other, less convenient sources.

Farmer Joe Dictyostelium

by Elio

A scanning electron micrograph showing the various stages of
transformation of Dictyostelium. Each body represents a different
stage in the process. Hundreds of thousands of single cells
aggregate to form a migrating “slug” (lower left). Once the slug
comes to a stop, it gradually elongates to form the fruiting body.
[Courtesy of M. J. Grimsom & R. L. Blanton, Texas Tech Univer-
sity]. Source.

The practice of agriculture is not limited to humans: ants, termites, and snails all grow fungi, and who knows who else do something similar. But not many have claimed that such activities are to be found among simpler organisms. Now we have a report that slime molds have also gone down the road to agriculture. Dictyostelium discoideum, the best studied of the cellular slime molds, is a social amoeba that thrives by grazing on bacteria. Given ample bacterial food, these organisms grow as single cells. When food becomes scarce, they aggregate into pretty, differentiated fruiting bodies (called sorus, plural sori) consisting of a round mass of spores held up by a stalk. The spores eventually become dispersed, to repeat the cycle at a new site. The entire epic can be viewed in a dramatic documentary available here. (This movie is narrated in German, giving you the opportunity to hone your skills in that language.)

Naegleria’s Split Morphology Disorder

by Psi Wavefunction

The complex structure of flagellates. EM section through
a mature flagellate Tetramitus. K1 = kinetosome. Cm =
cytostomal canal. FV = food vacuole. Rz = rhizoplast.
Source.

By default, a membrane-bound entity like a cell should be a spherical, formless blob. However, most cells are not such formless blobs, but rather have adopted one or more forms from a vast repertory of stunningly complex morphologies. To wit, see (and admire) the radiolarians, metazoan neurons, giant parabasalians or the endlessly weird and sophisticated ciliates. Even prokaryotes have a highly complex cellular structure, and are not, as some biochemists are prone to think, mere bags of enzymes. The deeper you venture into the realm of cellular diversity, the more awe-inspiring becomes the cornucopia of cellular structural and morphological variety. Luckily, there is some order to it as there are two fundamental 'genres' of cellular morphology, at least in the protists: flagellates and amoebae. Of course, there are also cysts, but since those are mostly resting stages (being a round ball isn't particularly helpful while feeding or fleeing from predators...) they can be ignored for now.

Cell shape depends on the cytoskeleton. As you know, its two main component systems are actin and tubulin, ignoring the plethora of miscellaneous proteins that are used for various structural jobs. Tubulin makes microtubules, the spindle fibers of mitosis, but is also important for the flagellar apparatus (we've yet to find one composed of actin and probably for good reasons). You also know that actin is a key player in cell motility and morphology in animal systems. It is also heavily involved in endomembrane trafficking within a cell, as well as endo- and exocytosis. If interested, a recent issue of Science has a nice overview of actin in morphogenesis and cell movement.

The role of the cytoskeleton in morphogenesis is much less clearly defined. It depends largely on the species. Plants, for example, rely very heavily on tubulin for morphology, with actin being a minor player. Amoeboid cells are primarily actin-based. In fact, amoeboid cells resort to tubulin largely for spindle formation during mitosis. They hate tubulin about as much as plants hate actin. Actin-based cells don't have to be amorphous; they are still able to achieve complex morphologies. But there is a positive correlation between amoeboid-ness and actin-ness ('actinity'?).

In contrast, flagellates are primarily tubulin-based. Of course, they still use actin for some intracellular work, but the shape depends largely on the whims of their microtubules. Perhaps not relying much on flagella allows the amoeboids to dispense with the microtubule organization pathways, thereby switching to actin. Flagellates, relying heavily on intact tubulin systems, may be less prone to losing their structure. Also, if you're a flagellate, you need shape for a modicum of streamlining. Try swimming around as a formless or floppy blob of some sort! Keep in mind that life at that scale is very different. Viscosity calls the shots when considering unicellular motility. Perhaps being hydrodynamic isn't even as important as simply retaining shape. Otherwise you'd be like a blob of molasses trying to swim through a sea of maple syrup. Not gonna get very far.

Whatever the reason, amoeboid cells tend to have a predominantly actin-based cytoskeleton, flagellates have a penchant for tubulin. Of course, not all organisms are decisive enough to make this commitment, so we've got amoeboflagellates in the middle.

Plenty of other organisms fancy transitioning between being more amoeboid or more flagellate. But few cells actually dispense with flagella and basal bodies altogether, to form them anew when special conditions arise. It's time to introduce one that does.

Genomic Secrets of P. infestans, the Master of Potato Blight

This is the third and final post for our week of the oomycetes. In our first post, Elio provided the foundation by answering five key questions about this often neglected and misunderstood group. This was followed by a reminder from Mercè Piqueras of the role one member, the potato blight pathogen, has played in our history. Here in this final offering, Merry explores what we now—more than 150 years after The Great Famine—know about this pathogen's tactics from its genome sequence.

by Merry

No fungicide has ever been found to which P. infestans could not ultimately adjust…Indeed, no potato has ever been developed with defenses that Phytophthora could not ultimately breach. (Glenn Garelik. Source)

More than 150 years after the historic Irish potato famine, the deadly pathogen responsible for potato blight, Phytophthora infestans, is now destroying more than $3 billion worth of potatoes each year. What is the secret of it's pathogenic success? Hoping to find some answers in its genome, a team of 96 researchers have sequenced virtually its entire 240 Mb genome. This is by far the largest and most complex genome sequenced among the chromalveolates, a diverse eukaryote supergroup that includes not only the stramenopiles (the oomycetes, diatoms, and some algae) but also the dinoflagellates and the apicomplexans.

Why so much DNA? That's more than double that of Caenorhabditis elegans.

A Mold That Changed the Course of History

In this, the second of our three posts focusing on the oomycetes, we are pleased to offer a post from the blog by Mercè Piqueras, La lectora corrent (The Common Reader), translated here from Catalan.

by Mercè Piqueras

Micrograph of an oospore of Phytophthora
infestans. Source.

Recently, Nature published an article about the genome sequence and analysis of Phytophthora infestans, the oomycete that caused the potato blight in the nineteenth century that changed the course of history. Phytophthora infestans is the reason that today about 11% of the population of the United States is of Irish origin and that the population of Ireland was lower at the end of the 20th century than it had been in the first half of the 19th century.

Symptoms of potato late blight on potato
leaves. Source.

People who migrated to the United States in the 19th century did so for the same reason that pushes many people to migrate today to Europe from Latin American or African countries: to improve their living conditions, sometimes simply to survive. Hunger to the point of starvation was the main cause that pushed many Irish to go to the United States. That hunger even has a name of its own: The Great Famine in English and Am Gorta Mór in gaèlic The cause was potato blight, a pest that is still difficult to control today, although there are several ways to try to prevent it. Potatoes, originally from the Andean regions of South America, were introduced in England in the mid-16th century by Sir Walter Raleigh, who planted them in the fields of his estate in Ireland. In the 17th century the crop spread throughout the island, supplementing the Irish diet that had consisted mainly of cereals and dairy products. By the early 18th century, potatoes had become the staple food of the poor during the winter, and its culture became more and more widespread.

Five Questions About Oomycetes

by Elio

We recently reprinted an article by Patrick Keeling entitled Five Questions About Microsporidia. His fine discussion prompted us to attempt a similar examination of another highly important—but oft-neglected—group of microbes, the oomycetes or water molds. We will post three articles, the first one (herewith) describing oomycete biology, the other two focus on a particular oomycete: the late potato blight pathogen. There we will recount a bit of Irish history and then discuss aspects of the pathogen's genome.

What Makes Oomycetes Important to People?

Saprolegnia infection on the body of a koi fish.
Source.

As you know, the potato blight caused widespread famine in potato-dependent, mid-19th century Ireland. You may also be aware of a current malady, sudden oak death, that affects large numbers of trees in the Pacific coastal states of the USA. And if you are involved in agriculture in any way, you have likely heard of the downy mildews of lettuce, onions, spinach, strawberries, and other crops. Likewise, those concerned with aquaculture are alert to a variety of "fungal" diseases, including one called saprolegniasis that causes about a 10% mortality in pond-grown salmon.

What do these diseases have in common? They are all caused by oomycetes, a large group of organisms that resemble fungi morphologically but are distant from them phylogenetically. Pathogenic oomycetes cause massive destruction and huge losses in agriculture and aquaculture. They infect many animals, among them fish, crayfish, and mammals—including humans. Oomycetes, along with chytrid fungi, are thought to be involved in the current global decline of the frog populations. Since some oomycetes prey on pathogenic fungi, they are considered candidates for biological control of fungal infections of plants.

Because of their impact, much effort has been devoted to elucidating the genetics and biochemistry of particular oomycetes. Likely the best studied one is the agent of the potato blight, Phytophthora infestans. The literature about this organism is indeed impressive, commensurate with this organism's accomplishments as a pathogen.

The Genes, The Whole Genes, & Nothing But The Genes

by Merry

SEM of Oxytricha in the process of reproducing.
Source.

We have come to expect the unexpected of ciliates, and Oxytricha trifallax, with its genomic capers, does not disappoint. Like many of its more famous ciliate relatives (e.g., paramecium, tetrahymena, stentor), Oxytricha is a complex unicellular organism with many specialized cellular structures. Of course, they have the requisite cilia for locomotion, feeding, and sensing their environment. But they also have a "mouth," food vacuoles where digestion takes place, kidney-like contractile vacuoles for osmoregulation, and a pseudo-anus—the cytoproct. Not surprisingly, ciliates tend to be large cells, some measured in millimeters. Combined with a fast rate of growth, this may require more gene transcription than a diploid genome can support. To cope with this demand, ciliates employ a convoluted strategy, one unique so far to this group.

Life in a Big Mac

by Merry

IFs make it to the Mac. Image of P. caudatum
fed a mixture of prey bacteria (green) and IFs
of H. obtusa (yellow). The IFs (arrow) are in
the Mac, the prey bacteria in food vacuoles.
Bar: 25 μm. Source.

From the bacterial point of view, a paramecium is a microcosm offering several tempting niches for colonization. When you collect a paramecium from nature, it's likely to have hundreds—even thousands—of bacterial endosymbionts on board, in different locations. Some will likely be in the cytoplasm, others in other cellular compartments, including the nuclei. To remind you, the ciliates evolved their own particular approach to nuclear compartments. They have two kinds of nuclei, macronuclei (we'll call them Macs) and micronuclei (Mics), typically two or more of each. The Macs carry out all the RNA transcription during normal vegetative growth; the Mics transmit the germline genome to subsequent generations. Both the Mics and the Macs are hosts to specific symbionts. While locations in mitochondria and nuclei have been observed for bacterial pathogens of animal cells, they are relatively uncommon.

So far, nine endosymbionts are known to live within the nuclei of paramecia, about half in the Mics, half in the Macs. These nine species, α-proteobacteria all, have been lumped together into the genus Holospora because of their similar cytology and lifestyle. Their closest known relatives are Rickettsia and Ehrlichia. They all appear to be obligate endosymbionts, i.e., are not known to live outside their hosts. All are host-specific and nuclei-specific.