Small Things Considered

Microtubules in the Verrucomicrobial Closet

by Daniel P. Haeusser

Figure 1. Global phylogeny of the tubulin superfamily. Source.

General biology textbooks, like the one I use for teaching, often depict the prokaryotic cell as an oval of homogenous-appearing cytoplasm surrounded by two membranes. This simplified image of a Gram-negative bacterial cell contrasts with the depiction of a well-organized, feature-laden eukaryotic cell with its membrane-bound organelles. While many would agree that the absence of a membrane-bound nucleus defines the prokaryotic–eukaryotic boundary, the recent decade of research has given us a glimpse of the actual organizational complexity of bacteria, which includes encoding cytoskeletal elements. Just as eukaryotes have their tubulin, actin, and intermediate filaments, the prokaryotes have FtsZ, MreB, and crescentin (although the occurrence of each varies greatly).

The first of these prokaryotic cytoskeletal proteins to be discovered, FtsZ, is a distantly-related member of the tubulin family (Figure 1). FtsZ is a highly conserved protein involved in cytokinesis in most bacteria, certain archaea, chloroplasts, and in the mitochondria of some protists. Although FtsZ shows only ~17% amino acid identity with tubulin, their crystal structures are remarkably similar (a fine example of structure trumping sequence).  Notably, FtsZ, unlike tubulins, is unable to form microtubule-like structures; instead it just self-associates into loosely bundled protofilaments. Although a recent paper shows that FtsZ forms tubule-like structures in vitro in the presence of a binding partner/assembly regulator, these tubules are quite distinct from eukaryotic microtubules in both size and structure, and their in vivo relevance is uncertain.

Green Flypaper

by Merry

Source.

Troubled by pesky flies in your home or office? Tempted to reach for the toxic flypaper? Here’s a green alternative long known by the Indians of the Central Mexico highlands. Step outside and look around for a tree with entire branches covered by a large spiderweb. Clip out a section of the web and hang it indoors, complete with resident spiders. A natural fly trap. Common house flies will be attracted to the web, lured to their death by a sweet smelling bait with a microbial source.

Make certain, though, that you’ve got the right kind of web. Only those made by the social spider Mallos gregalis, will work. Social spiders? Granted, most spiders are cannibalistic loners, but approximately 23 of the 39,000 spider species have opted for varying degrees of permanent, non-territorial sociality (quasisociality). The spiders in these casteless communities cooperate in hunting, feeding, nest construction, and, in some cases, caring for the spiderlings, as well.

The Paenibacillus Moving Company

by Elio

Enlightenment, a bacterial colony. Displayed in the
Esher Ben-Jacob online art gallery. Source.

Microbes get around. They can be carried by the wind, by insects, or by water currents, sometimes across large distances, sometimes from one grain of soil to the next. Some bacteria contribute to their own dispersal by their motility or, rarely, one may think, by the motility of other microbes. It’s hard to generalize here because there are just too many variables, too many conditions where microbes are on the move. But this business can be pure fun. So it’s with pleasure that I read about a delightful account of how bacteria can transport fungal spores to the benefit of both.

But first a little background, both microbial and personal. Some bacteria, when placed on an agar surface, do not stay put but spread out from the point of inoculation. Certain ones, such as Bacillus mycoides, do it simply by extending their long filaments, but others do it by moving on the agar surface. There are several ways to move along, either with flagella (a process called swarming) or without them (e.g., gliding or twitching). Swarming, whether in Gram-positives like certain Bacillus species or in Gram-negatives such as Proteus, is a communal activity. Single cells don't swarm, aggregates of several cells do. What you see under the microscope are rafts of bacteria arranged side by side, moving along a path that is sometimes regular, sometimes not. To download a movie of a ‘raft’ of ceils swarming together, click here (or to go to the web page where you can select additional file 4, click here). The speed of movement across the agar surface is pretty amazing, about 180 µm/min or 10 mm/h. This means that if you place such a bacterium in the center of a 14 cm Petri dish, it will reach the edge in about seven hours. When such a swarm has covered a certain distance, the cells either stop moving, as in the case of Proteus, or make round disc-like colonies that have the odd ability to rotate. For a movie of a ‘colony’ of cells swarming together, click here (or to go to the web page where you can select additional file 2, click here). The speed at which this rotation happens is also quite fast, one revolution in about 10 seconds. Towards the end of my career, but while I still had a lab, my collaborator Dana Boyd and I played around with these organisms. This was the last time that I worked at the bench, so I quite cherish this topic.

Talmudic Question #83

Assume the Earth is hit by a large asteroid that lowers the average temperature of the planet to the extent that would eliminate most multicellular life. What would be the short term consequences for the microbial world? And later on?

Pushing the Thermodynamic Envelope into the Proteomic Edge

by Tracey McDole

A schematic potential energy funnel for the folding of
proteins without sufficient water present. It highlights the
many barriers to the preferred minimum energy structure on
the folding pathway. There are numerous local minima that
might trap the protein in an inactive three-dimensional
molecular conformation. The top rim represents the high
energy of the unfolded protein, with folding lowering the
energy towards a minimum energy structure that is at the
bottom of the funnel. It should be noted that this funnel
represents a three-dimensional landscape, whereas the
actual energy landscapes are multidimensional. Source.

The word marginal means to be at the outer or lower limits; minimal for requirements; almost insufficient. Certainly being marginal sounds bad, but is it always? In a recent issue of PNAS, Dill and colleagues show that the proteome—a cell’s collection of thousands of different types of proteins—is only marginally stable to denaturation under normal physiological conditions. Little did you know, we’re all just a few kcal mol^-1 away from being a pile of unfolded proteins.

Just exactly how close are we to becoming a marinade of melted matter at 37.5 °C? The answer lies in the distribution of lengths of our proteins. This is because the dynamics of protein folding largely depends on just one factor, the number of amino acids in the protein (N). In other words, at a given temperature and pressure, a number of fundamental thermodynamic properties scale linearly as a function of amino acid chain length. So, if you want to visit Uncle Thermophile in Yellowstone, you better pack plenty of short proteins. This is unexpected, considering that most important characteristics of proteins (e.g., native structure and biochemical mechanism), depend much more on the details of design—things like the number of hydrophobic amino acids or hydrogen bonds, counts of salt-bridging ion pairs, or structure, both secondary and tertiary.

That Scary Restroom Microbiota

by Elio Schaechter and Joshua Fierer

Source.

Newspapers and other media are reporting with regular frequency that restrooms, ATM machine pads, money bills, and other sites carry many different microbes upon their surfaces including potentially pathogenic bacteria and viruses. Headlines call attention to such scary-sounding news and alarm the general public. We can expect that this practice will engender a widespread concern of the public for their safety. The outcry will encourage the implementation of unreliable, unnecessary, and potentially counterproductive “protective” measures. People may, for example, resort to using soaps with bactericidal compounds that have the potential to alter the generally protective normal flora. Inappropriate or non-essential use of bactericides may well accelerate the development and spread of resistance to microbicides and antibiotics within the microbial community. Resistance capabilities, including the upregulation of efflux pumps, can evolve particularly rapidly, and these same mechanisms may also increase resistance to antibiotics. For a reference to this topic, click here.

Let us suppose, as implied by these reports, that we do often encounter potential pathogens on ‘fomites,’ that is, inanimate objects. This is nothing new.

It’s Raining Viruses!

by Merry

Caterpillar cadavers containing viral particles (OBs) are
eaten by predatory invertebrates such as this spider.
Since the alkaline pH of the insect midgut is required to
release the virions from the OBs, the OBs pass through
the predator’s digestive tract intact and are deposited
in their feces. In this way the virus gets a free ride across
relatively large distances, there to await ingestion
by a hapless caterpillar. Source.

It’s true! Each year it rains viruses, more than a trillion of them per acre over thousands of forested acres in the USA. This is the work of the airborne arm of the USDA Forest Service, part of their efforts to reduce the devastation to hardwood forests caused by the imported gypsy moth, Lymantria dispar. Each year they spray with a registered “general use pesticide” called GYPCHEK, the active ingredient of which is Lymantria dispar multinucleocapsid nuclear polyhedrosis virus (LdMNPV), an ideal ‘green’ pesticide. The virus is host-specific, self-replicating, biodegradable, and deadly. And I would add, it makes a most interesting story, provided you’re not a caterpillar.

LdMNPV is a member of the genus Alphabaculovirus, family Baculoviridae. These viruses infect arthropods, most commonly lepidopteran larvae—what you and I would call caterpillars. Because one virus can efficently convert one caterpillar into more than 10⁹ viruses, with each of those progeny poised to repeat the process, they have received attention as potential biological control agents to help us in our perpetual war against the insects.

SEM of baculovirus OBs (polyhedra). Arrows
indicate three polyhedra of different sizes.
Bar = 2 μm. Source.

Viruses are supposed to be small, something you look at with an electron microscope. But these viruses form unusually large polyhedral particles that range in size from 0.15 to 15 μm, thus are readily visible at 400× or 100× magnification. The particles, called occlusion bodies or OBs, are how the virus journeys from one caterpillar to the next. An OB is made up of many virions embedded within a stable, paracrystalline protein matrix. Nested inside each virion are several rod-shaped nucleocapsids, a nucleocapsid being a protein shell enclosing a copy of the viral genome. The whole conglomeration is assembled in the nucleus of the host cell. Thus the multinucleocapsid and the nuclear in the virus’s name. What about the polyhedrosis? This is a general term for any disease of caterpillars that is caused by polyhedral virus particles and that leads to the gruesome liquefaction of the host and the accumulation of OBs in the fluid.