Small Things Considered

Are Phages the Answer?

by S. Marvin Friedman

The emergence of multiple drug-resistant bacterial strains, the prevalence of recalcitrant biofilm configurations, and the reluctance of the pharmaceutical industry to initiate new antibiotic discovery programs have led to the development of a formidable population of bacterial pathogens that is increasingly difficult to control. After a long but successful era of research that had all but eliminated serious threats from bacterial infections, we are now facing this dire problem once again. In response, researchers have recently been exploring alternative approaches to antibiotic therapy including identifying chemical agents that antagonize quorum sensing and thus prevent population-wide expression of virulence genes, as well as employing either intact bacteriophages or their isolated lysins to directly kill their pathogenic bacterial hosts. Lysins kill Gram-positive bacteria by hydrolyzing the peptidoglycan in the cell wall, thereby causing cell lysis. Gram-negative bacteria are immune to their action because their outer membrane does not allow the lysins access to their peptidoglycan. I will now summarize two recent papers that use intact phages to combat two important bacterial pathogens, both in vitro and in vivo.

Pseudomonas. aeruginosa colonies showing the
characteristic green color. Source: Gloria Delisle,
Microbe Library, ASM.

One of the important applications for phage therapy is for treating cystic fibrosis (CF). CF is an inherited genetic disorder where a defective enzyme results in the production of unusually viscous, sticky mucus and chloride-containing secretions in ducts and body cavities. The lungs, in particular, are seriously compromised and are readily infected, typically by Pseudomonas aeruginosa. Initial colonization usually occurs during early childhood. The ensuing chronic infection eventually causes death due to respiratory failure in 80–95% of CF patients. Treatment of these patients is impeded by the multiple mechanisms of antibiotic resistance harbored by these strains of P. aeruginosa and by their ability to form biofilms in the lung.

What Is This Link to Mushrooms in Works of Art?

by Elio

Pseudo Fardella, Italian, active in Tuscany second half, 17th
century. A Basket of Cherries, Apples, Plums, Chestnuts,
Asparagus and Porcini on a Ledge. Private collection.

On the left side of this blog, in amongst the Blogroll links, is a somewhat strange entry, “Mushrooms in Works of Art.” I’ll save you the trouble of clicking on it. This is the website of a registry that lists works of art, mainly Western, that display mushrooms. Now, why would anyone care about this? The project started about 10 years ago when mycologist Hanns Kreisel from Greifswald University in Germany and chemist Tjakko Stijve from Switzerland and I came together, impelled by the same thought, which was that depictions of mushrooms in art would give us some insight into their relationship to people of various times and cultures.

On Retrons

We reprint this article from Habib Maroon’s blog Biobabel, with his kind permission.

by Habib Maroon

The secondary structure of msDNA Ec73. The
76 nt RNA (in box), is joined to a 73nt ssDNA.
Note the 2'-5 phosphodiester bond connecting
the two molecules at the branching guanosine.

Retrons are an understudied type of prokaryotic retroelement responsible for the synthesis of an enigmatic species of small extra-chromosomal satellite DNA termed multicopy single-stranded DNA (msDNA). msDNAs are actually composed of both a single-stranded (ss) DNA and a ssRNA. The 5' end of the msDNA is covalently bonded to an internal guanosine residue of the msRNA by a unique 2'-5' phosphodiester bond, whilst the 3' ends of the molecules are joined by a small stretch of base-pairing. msDNAs are therefore a sort of looped hybrid molecule, but extensive internal base pairing creates various stem-loop/hairpin secondary structures (see figure). The retron, (i. e., the genetic loci encoding the msRNA and msDNA molecules (msr and msd) and the gene encoding the reverse transcriptase (ret) responsible for the synthesis of msDNA) is transcribed as an operon.

Retrons are present in a wide variety of eubacterial, and some archaeal, genomes. A recent study identified 97 different retron-like reverse transcriptase genes within bacteria, however their distribution is sporadic. For instance, seven distinct retron elements have been found amongst E. coli strains, but only 15% of natural E. coli isolates produce msDNAs. Based on their sporadic occurrence and analysis of codon usage, retrons have been suggested to be a recent addition to the E. coli genome.

The Winner of the 2012 Peter Wildy Prize: Vincent Racaniello

by Elio

The winner of the 2012 Peter Wildy Prize For Microbiology Education is Vincent Racaniello of Columbia University, a fellow blogger (Virology Blog) and the podcast host of TWiV (This Week in Virology), TWiP (This Week in Parasitism), and TWiM (This Week in Microbiology).

This prize is awarded annually by the Society for General Microbiology (UK) for an outstanding contribution to microbiology education, without restriction on the area of microbiology in which the award is made. This may include university teaching or education of the general public, school pupils or professional groups. The winner receives £1000 and gives a lecture on his/her work at a Society meeting. Vincent’s talk to the SGM was entitled Educating the World about Microbes and can be heard by clicking here.

Frankly, I can't think of anyone more deserving of this award. Vincent, with whom I have had the pleasure of working on TWiM, is a consummate master of communication. Seldom in my experience have I met a scientist who can deliver the pleasures of science in such an articulate way. To listen to him is to become enthralled with whatever it is he is talking about. I can bear witness to his fervor, his gentleness, his humor. The French have an expression for it: un homme engagé (roughly translated, a committed man). Vincent is indeed engagé!

The Immunological Synapse Goes Viral

by Merry

Structural proteins in the HTLV-I virion include Gag (a
capsid protein) and Env (the surface glycoprotein required
for infectivity). Fluorescently-labeled antibodies showed
that these proteins were not polarized in isolated infected
T cells. In cell-cell conjugates, the proteins accumulated at
the cell-cell junction within 40 min. This particular confocal
image shows polarization of HTLV-I Gag p19 (red) to the
cell-cell junction. Source.

Here’s yet another tale of how a cunning virus has converted one of our antiviral defenses into a tool for its own purposes. The co-opted mechanism is one used by cytotoxic T-cells to kill virus-infected cells: the immunological synapse. More on this in a moment. The virus is Human T-Lymphotropic Virus Type I (HTLV-1). The appropriated tactic enables the virus to spread efficiently to new host cells.

When discovered in 1977, HTLV-1 was the first known human retrovirus (HIV not being identified until six years later). While not as devastating as HIV, it currently infects 10–20 million people, 2–3% of whom will develop adult T-cell leukemia/lymphoma while another 2-3% develop a chronic inflammatory condition (HAM/TSP). Like HIV, it infects primarily CD4+ T cells. And like HIV, HTLV-1 also transmits from one person to the next in blood, milk, or semen. But just how it does this was puzzling because, unlike HIV, few free virions are found in the blood and, of those, only one virion in a million is infectious. More clues: Only enveloped HTLV-1 virions are infectious and they acquire their envelope from the lymphocyte plasma membrane as they bud from their host cell. Efficient transfer of the virus between cells requires cell-cell contact, both in vitro and in vivo.

Combined these observations suggest that perhaps the virions bud from one cell and immediately enter their next host cell without ever wandering free in the liquid milieu. What would such a strategy require? First, an infected CD4+ T cell must dock with an uninfected CD4+ T cell, something it normally does not do. The mature virions in the infected cell must be transported to the zone of surface contact and be released there, acquiring their envelope as they exit. The now-infectious virions must then enter their new host cell directly.

Talmudic Question #86

Given that so many kinds of bacteria are intimately associated with animals and plants, why are so relatively few pathogenic?

Oddly Microbial: Ribocytes

by Marcia Stone

Michael Yarus’s book, the basis for this article.

Ribocytes, our 4-billion year old RNA ancestors, were quintessentially microbial, quite different though than modern cells which eventually out-divided most of these little creatures and probably ate the rest. But while they were here ribocytes ruled the world—inventing both the genetic code and protein synthesis during their reign. The fact that today’s organisms still depend on RNA to carry out fundamental biochemical processes proves how durable such ribocytic inventions were.

“The genetic code is an invention of the middle RNA period,” says Michael Yarus at the University of Colorado in Boulder in his book Life from an RNA World: the ancestor within. Once reproducible RNA sequences were in place, riboenzymes, or ribozymes, were developed and replication began in earnest. “The RNA world appears in its definitive form when RNA learns to replicate and, as a result, Darwinian evolution begins,” he adds.

Wily Phage Trumps Host Toxin

by Merry

Source.

Toxin-antitoxin (TA) systems are a dime a dozen. They are found on plasmids and chromosomes within many prokaryote groups—even those with an intracellular lifestyle. Each is a two-gene operon, one gene encoding a toxin protein, the other the cognate antitoxin. Key to their function is the differential stability of the two gene products, the antitoxin degrading more rapidly than the toxin. When both the toxin and the antitoxin are present in the cell, all is well. They interact and the antitoxin neutralizes the toxin. When production is halted, the toxin outlives the antidote and then kills the cell (or at least inhibits its growth). TA systems carried on plasmids have earned the epithet addiction module. If a host cell jettisons the plasmid, it is dead, thus guaranteeing the maintenance of the plasmid in the host cell lineage.

That these modules are so often carried on bacterial chromosomes suggests they are useful for the bacterium. They have all the makings of an effective defense against phage infection. Here’s why. Typically, an invading phage rapidly shuts down host protein synthesis. If the host carries a TA system, on either its chromosome or a plasmid, cell suicide would quickly follow and phage replication would be thwarted. That particular host cell would die, but in so doing it would protect its siblings nearby by preventing the release of progeny phages.

Living On the Edge…of the swarm

by Gemma Reguera

The edge of a wave, a tsunami wave that is. Source.

If anybody knows how to move, it’s bacteria. They swim in liquids using rotating flagella, but they also know how to twitch, glide, and slide on surfaces. The mechanisms that power their surface motility are varied, ranging from energy-intensive processes such as the extension and retraction of type IV pili (twitching) to movement via focal-adhesion complexes of the cell’s outer surface (gliding) or growth-induced translocation aided by surfactants (sliding). Some flagellated bacteria can also use the rotating motion of the flagellum to move across moist surfaces, a process known as swarming motility. As the word indicates, swarming is a collective behavior. Swarming cells move side-by-side in regular or irregular formations known as rafts or swarms. See, for example, previous blog posts showing the regular rafts produced by Paenibacillus or the distinctive, irregular terraces formed by Proteus. And even E. coli does it, too!

Despite their close proximity, the cells within the swarms do not attach to each other, nor do they adsorb to the surface. They swim across a thin film of liquid that is drawn out of the underlying surface; they rely on random collisions with neighboring cells to reorient themselves and to coordinate the collective motion (pretty much like the random movements of sheep within a flock). Cells at the swarm’s outermost edge truly live…well…on the edge, stuck between the liquid boundary and the force of the spreading swarm. Time-lapse microscopy shows that most of these cells slow down and even stall. Sometimes they reverse their direction to face inwards and become stuck to the substratum. However, these cells eventually get free and swim back to the center or along the edge of the swarm, suggesting that they continue to rotate their flagella while stalled. But could this be proved?