Small Things Considered

TWiM #45: Secreted nucleic acids RIG a STING

Hosts: Vincent Racaniello, Michael Schmidt, and Elio Schaechter.

Vincent, Michael, Elio review innate immune sensing of Listeria secreted bacterial nucleic acids, and how Wolbachia enhances egg production in Drosophila.

Right click to download the audio file. (52 MB .mp3, 71 minutes)

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Talmudic Question #93

by Paul Evans

Which  bacteria besides the rhizobia undergo terminal (irreversible) differentiation?  (no fair saying 'spores')

The Slime That Smiles

by Heidi Arjes

Figure 1: Cell death occurs between the emerging digits during development. A fluorescent chemical was used to visualize regions of cell death in these embryonic mouse limbs. Source.

Have you ever wondered how individual fingers form? If you have taken a developmental biology class, you know that the hand first develops as a mitten-like structure with the future fingers connected (Figure 1). Later, during normal development, the cells in the areas between the fingers undergo programmed cell death, and thus leave behind five fingers on each hand. Programmed cell death is important not only in development and long term viability of animals, but also plays a role in unicellular organisms. For example, in the social amoeba Dictyostelium, a subset of cells undergoes a type of programmed cell death similar to autophagy to form fruiting body stalks. The remaining dead cells in the stalk are highly vacuolated and provide support for the spore body (figure 2).

Art on a Dish

by Elio

Fleming was one of the first to explore microbial art by creating “germ paintings” using living bacteria. Source.

Quite a few years ago, I spent some time viewing a natural history-inspired show at the Boston Museum of Fine Arts. One exhibit that especially caught my attention consisted of a meter-square dish containing what must have been EMB agar. This “plate” had been left exposed to the air and the ensuing mold colonies were allowed to grow until they became confluent. The result was stunning: individual molds displayed their natural colors plus those of the dyes (methylene blue and eosin) they selectively picked from the medium. The result was a riotous jumble of exceptionally vivid colors, from blues to reds.

Darwin, as portrayed on agar using E. coli, by students in the Gregory lab. Source.

Although such “microbial art” is impermanent, it has had its adherents since the early days of agar plates. In fact, Alexander Fleming “drew” portraits, and even a pair of phage particles fighting. He inoculated the plates using pigmented bacteria and incubated the plates until growth became evident. To quote from this website Apparently he prepared a small exhibit of bacterial art for a royal visit to St Mary’s by Queen Mary. The Queen was ‘not amused and hurried past it’ even though it included a patriotic rendition of the Union Jack in bacteria.

Virus in the Room

I am the Lorax, I speak for the trees. I speak for the trees, for the trees have no tongues, and I'm asking you, sir, at the top of my lungs.
– from The Lorax by Dr. Seuss

by Welkin Johnson

Figure 1: A non-virus. Source.

As biologists, we divvy the biological realm up into domains using a formula that frankly, smacks of nepotism, bestowing three glorious domains upon our closest relatives—the Eucaryota, the Archaea, and the Bacteria—while committing an injustice to the so-called viruses, lumping them together in a miscellaneous catch-all category (“viruses” from Latin for poison and other noxious substances) with contemptible disregard for phylogeny or any true measure of diversity.

Imagine that viruses, like Dr. Seuss’s Truffula Trees, had a vocal advocate like The Lorax. Undoubtedly, through the agency of their outspoken mouthpiece, they would protest these gerrymandered borders and laugh at our skewed notions of biological diversity. After all (the viruses would argue), just consider the platypus, the coelacanth, the earthworm, and the bacillus. All these organisms have double-stranded DNA genomes, whose lengths all fall within roughly the same order of magnitude, which they replicate using evolutionarily customized versions of what amounts to the same basic enzymatic apparatus. How boring! How unimaginative! Now consider this (the viruses go on to say): the giant Mimivirus, 1256 nm of girth enfolding >1,000,000 base pairs of DNA, and the tiny Circovirus, with a mere 1,800 bases of single-stranded DNA tucked inside a 20nm-wide shell, are neither more nor less related to one another than either one is to an elephant! (For those who are not familiar with the elephant, it is a relative of the platypus, the coelacanth, the earthworm, and the bacillus)

A Bacterium Learns Long Division

by Nanne Nanninga

The common picture of a dividing rod-shaped bacterium encompasses the positioning of the divisome, including an FtsZ-ring, in the cell center. This occurs after the cell has doubled its length without increasing its diameter. Conversely, increase in diameter without cell elongation would seem highly unlikely in a rod-shaped organism. Yet, this happens.

Figure 1: SEM of tightly apposed ectosymbionts on the surface of L. oneistus. Electron micrograph by N. Leisch.

In fact, this is the normal condition for an ectosymbiotic bacterium that lines the surface of the marine nematode Laxus oneistus. The symbiont is a g-proteobacterium like E. coli, but unlike E. coli it has not been cultured outside its natural habitat. As originally described by Polz et al. in the early nineties, the bacteria are positioned perpendicular to the surface of L. oneistus. They are glued to the surface of the nematode by a C-type lectin. The original paper already indicated that division takes place longitudinally, with one of the daughters presumed to remain attached to the nematode. This makes sense because otherwise the daughter cells would get lost to the environment. Recall that this phenomenon lies at the basis of the Helmstetter-Cooper baby machine, whereby one of a pair of newborn cells is selected to start a synchronous culture (Helmstetter et al.)

Recently, Leisch and colleagues have extended these observations by carefully determining cellular dimensions and visualizing the FtsZ division protein with fluorescent E. coli monoclonal antibodies. The results can be compared with E. coli data (Figure 2A, B). Whereas E. coli elongates as expected, this is not what happens with the symbiont. The symbiont does not change its length (Figure 2A) but increases its diameter (Figure 2B). Consequently, the symbiont divides longitudinally, (Fig. 2 C-H). Immunostaining of FtsZ reveals that FtsZ positioning correlates with the cell constriction. In fact, an ellipsoidal FtsZ-ring is observed stretched along the length of the endosymbiont.

Why Listeria Is Competent to Be Virulent

by S. Marvin Friedman

A listeriosis outbreak of 2011 caused 147 cases of illness and 33 deaths in 28 states in the US. The source was cantaloupes grown at one Colorado farm. Source.

It is downright scandalous that in our hi-tech world food-borne infections should be so prevalent (some 48 million cases a year in the US alone, with about 3000 deaths). The tools to take care of these problems are hardly mysterious, requiring mainly safe food production and preservation. High on the list of bacterial offenders is Listeria monocytogenes, a Gram-positive facultative intracellular pathogen that is acquired through ingestion of contaminated food or fluids. Listeria is found in uncooked meats, vegetables, fruits such as cantaloupes, unpasteurized milk and milk products, and some processed foods. Although pasteurization and sufficient cooking will kill Listeria, contamination often occurs after cooking and before packaging. Listeriosis is a disease primarily affecting pregnant women, newborns, adults with compromised immune systems, and the elderly. The two most common life-threatening symptoms are sepsis and meningitis. This is a serious disease with a relatively high mortality that can reach 25%.

L. monocytogenes is an intracellular parasite of epithelial cells and macrophages. It initially resides in a membrane-bound vacuole, the phagosomal vesicle, which is a dangerous site for many bacteria. In order to carry out a successful infection, it escapes into the host cell’s cytoplasm by lysing the vacuolar membrane via a pore-forming hemolysin, listeriolysin and two phospholipases. However, the precise mechanism of this escape is not fully understood. Once within the host cell cytoplasm, the bacteria replicate and use the host’s actin filament network to propel themselves within the cell and from cell to cell.

Talmudic Question #92

Does DNA do anything other than serve as a repository for genetic information?

The Excitement of Clinical Microbiology

by Elio

Members of the San Diego VA Clinical Microbiology lab: (L to R) Romelia Quinonez, Raymond Samson, Carlo Basallo, Monica Beach, Icela Gonzalez, Dr. Joshua Fierer, Juan Ybarra, Jasmine Estrada, Tracey Grosser, Laura Gomez.

Clinical microbiology, one of the major branches of microbiology, goes largely unnoticed by academics, in part perhaps because the diagnostic activities of microbiologists are pursued separately, in hospital and commercial labs. I’d venture to guess that many academic microbiology researchers have never set foot in one of these labs. Their loss, as it would be an exciting and rewarding experience.

This rift casts aside the historical roots of our field. At its beginning, soon after bacteria were found to be the cause of infection, there was a huge rush to develop methods for determining the identity of agents responsible for a patient’s illness. Ingenious laboratory media were designed to favor the growth of certain organisms and to reveal their distinguishing properties, and serological techniques were developed alongside. In those days, there was no significant distinction between diagnostic microbiology and the rest. In time, as research in other fields of microbiology matured, these diverged more and more from this point of origin.

A Whiff of Taxonomy: The Acidobacteria

by Elio

We occasionally post very brief taxonomic pieces on selected bacterial groups. Be warned that we may not be fully attentive to the taxon level and may mix up genera and higher taxa.

Phase-contrast and transmission electron micrograph of two soil isolates of members of the Acidobacteria, KBS 83 (A and B) and KBS 96 (C and D). The arrow in panel A indicates the capsular material layer produced by KBS 83. Scale bars indicate 1 μm (B and D) and 200 nm (A and C). Source.

The Acidobacteria are an offspring of metagenomics. Their existence as a phylum was not known until 1997, when their existence was first noticed using 16S rRNA techniques. But these are no obscure oddities living in extreme environments. Look for them in soils where they are among the most abundant bacteria, particularly in acidic soils where they make up 30-50% of all the 16S rDNA clone libraries. Belying their name, some of these organisms are found in alkaline environments, but the majority remains true to it and prefers a low pH.

Most Acidobacteria were hidden from us BM (Before Metagenomics) simply because they were part of the uncultured majority. The relatively few that have been cultured comprise about 1/1000 of the bacterial species in captivity. Their recalcitrance may reflect nutritional and physical predilections that are not readily satisfied in the lab. These organisms are distinctly oligotrophic: in the environment, they prefer poor soils to carbon-rich ones and their number decreases when soils are enriched with sucrose. Thus, you can “entice” them to grow in the lab under oligotrophic conditions, with best results being obtained when using a combination of low nutrient media, low pH and high CO2 concentrations in diffusion chambers. And patience helps greatly. When plates are sealed and incubated for weeks, colonies of Acidobacteria will show up.