Small Things Considered

A Few Thoughts About the 2012 San Francisco ASM General Meeting

by Elio

Golden Gate Bridge at Night. Source.

I recently returned from the ASM yearly general meeting in San Francisco. It happens to be 61 years, no less, since I attended my first such event, that one in Chicago. In those days, many members attended a giant banquet as part of the event, I well remember. As a poor graduate student, I couldn't afford the few dollars it cost, so I ate elsewhere. Lucky me; the entire assemblage of microbiologists came down with food poisoning!

Livestock Bacteria Are as Old as the Livestock They Kill

We are pleased to reprint here, with permission, a recent post from Thoughtomics, a Scientific American blog written by Lucas Brouwers. His subject matter? “Exploring evolution through genes, computers and history.” This particular post can be found here.

by Lucas Brouwers

Aurochs were the ancestors of domestic cattle. Photo credit:
Marcus Sümnick.

Animals were wilder then. Horns were longer, temperaments fiercer. These wild things had forever been free when humans took control of their flocks and herds, 10.000 years ago. Through careful breeding and rearing, the first pastoralists of the Near East moulded the beasts into more docile versions of their former selves. Over time, Bezoar became goat and auroch became cow. But it wasn’t just the beasts that changed. Somewhere deep inside their lungs, invisible to the human eye, a wild bacterium became livestock disease.

Fine Reading: Cnidarians and Dinoflagellates Together

by Merry

Zooxanthellae (brownish-green cells) inside translucent coral
polyps. CREDIT: © osf.co.uk. Source.

The very word infection brings to mind the arrival of a nasty pathogen countered by a host immune response, a battleground strewn with the carcasses of the losers. But how do you define infection? Is not the beginning of an endosymbiosis, even a mutually beneficial one, also an infection? Corals, anemones, and other Cnidarians have been infected for millions of years. They are among the numerous marine invertebrates that have established endosymbioses with photosynthetic partners, their partners being dinoflagellate algae of the genus Symbiodinium (commonly referred to as zooxanthellae, or zoox for short). While some Cnidarians pass their endosymbionts to their offspring, others have to be “infected” anew each generation. The intricacies of this relationship between Cnidarians and their dinoflagellates is the subject of an exhaustive review (424 cited references!) by Davy, Allemand, and Weis. Here you’ll find many questions to ponder, each presented as a mini-review that includes what is known,  the research that provided those answers, and current hypotheses about the remaining questions. Here is a sampling of those questions.

How an Endosymbiont Earns Tenure

by S. Marvin Friedman

P. chromatophora displaying its two chromatophores (CRs).
Source.

Plastids and mitochondria are organelles in eukaryotic cells that originated from bacterial endosymbionts via invasion or enslavement or a synergistic amalgamation, depending on your viewpoint. Since these events occurred more than one billion years ago, it has not been possible to trace the evolutionary steps in the transition from endosymbiont to mature organelle, a process referred to as organellogenesis. Enter the protozoan amoeba, Paulinella chromatophora. This protist may provide a “missing link,” a nexus between endosymbiosis and organellogenesis. Where does one draw the line between the two? It’s becoming more and more difficult to decide.

The road from temporary resident to obligate endosymbiont to organellar citizen is fraught with obstacles. Many proteins that do the work in today’s organelles are made on cytoplasmic ribosomes and then imported. The difficulties in evolving a protein import mechanism for an endosymbiont, wrapped as it is in multiple membranes of host and symbiont origin, was thought to be what made successful organellogenesis such an exceedingly rare occurrence. But Paulinella tells us this might not be so difficult after all.

A Table for Two

by Elio

TEMs of thin sections of infected V. vulnificus prey
cells. (A) Infected by phage only. (B) Infected by
BALO only. (C and D) Co-infection by both BALO
and phage. In (D) BALO did not change the shape
of the prey cell. B, C, and D show the bdelloplast,
the post-BALO infection structure with the predator
residing inside the prey cell. Bar = 500 nm. Source.

What fun, unless you are the one being preyed upon. Two predators, a phage and a “bacteriophagous” bacterium, simultaneously dine and reproduce in one host cell.

Doesn't this open a whole lot of questions, such as: How often does co-infection take place in the wild? Do the two predators “talk” to each other? Does this matter for the geochemical cycles? And, most important, who has first dibs?

Huan Chen and Henry Williams of Florida A&M University ask just such questions, using the marine bacterium Vibrio vulnificus as the prey, with both a phage and a BALO, Bdellovibrio-like organism (actually something called Cluster IX of Bacteriovorax) as predators. They mixed the participants in a predator/prey ratio of 1:1:1, let them work on each other, then looked at what was happening in thin sections under the electron microscope. The conclusion? The two predators do not seem to compete with one another, rather they both feast on the prey together. Both the invading bacterium and the phage multiply within the same host cell. This is a first.

Bdellovibrios and phages reproduce by very different mechanisms, but both require an intact host cell. Specifically, bdellovibrios penetrate the cell wall, reside in the periplasmic space, and shut off the host metabolic functions. They induce cell lysis after about 15 minutes, which is less than the time most phages require for their cycle. But the phage, it appears, is speedy enough to replicate in the time available. No doubt, there are some complex dynamics afoot.

This is a complicated business. Whereas each of the two predators has its own lifestyle with regards to cellular localization, reproductive strategy, and kinetics, co-infection makes special demands on each. Just how infection by BALO affects that of the phage and vice versa remains a fertile topic for investigation. Who says that things are simple in the oceans’ microbiome? The authors point out: Rather than the viruses and Bdellovibrio and like organisms competing for a single prey cell, both can survive in the same cell and successfully reproduce themselves. This is an especially valuable mechanism when the prey is in short supply, and the survival of the predators may be at stake.

The august (and relatively new) ASM journal mBio published this work in a section entitled Observations. This is a nice innovation for which the editors should be saluted.

Oddly Microbial: Cancer Cells

by Marcia Stone

Editor’s Note: This is the second in what is expected to be an ongoing series about cells that might not come immediately to mind when you think “microbe.” The first is linked here Oddly Microbial: Ribocytes. Comments and suggestions are encouraged.

“Cancer cells are ancient alternative organisms, living protozoan-like fossils, foreign to their hosts because of deep origins elsewhere,” says oncologist Mark D. Vincent from the University of Western Ontario in Canada. They are, he asserts “In the body but no longer of the body,” and therefore deserve a radically different taxonomy. This isn’t a new idea but one taking on increasing relevance with the dismal failures of one onco-therapy after the other.

Source.

Talmudic Question #88

How come viruses have developed so many different ways to penetrate into their host cells?

Retrospective, June 2012

We continue our semi-annual ritual and post this quick tour of featured blog postings since our December, 2011, Retrospective.

Source.

Viruses

It’s Raining Viruses! (Merry) Metabolic genes acquired from their hosts are one strategy used by baculoviruses to convert one caterpillar host into more than 10⁹ progeny viruses.

The Immunological Synapse Goes Viral. (Merry) Once again, a virus coopts some of the sophisticated functions of our immune system and turns them against us. In this case, HTLV-1 gains an efficient mechanism for cell-to-cell transfer.

Onboard a Flying Syringe. (Merry) Insect vectors carry viruses that infect our crops as well as us. Metagenomics provides a way to query the insects and find out who is onboard.

Wily Phage Trumps Host Toxin. (Merry) Toxin-antitoxin systems are part of the bacterial arsenal of anti-phage defenses, but phage T4 carries its own antitoxin.

Source.

Ecology

That Scary Restroom Microbiota. Josh Fierer and Elio take exception to the scary news headlines generated by a metagenomic study of bacterial DNA in a restroom. Bugs in a bathroom? Surprise!

The Paenibacillus Moving Company. (Elio) This master swarmer can carry cargo, in this case fungal spores. It can also move across space on bridges made of fungal filaments.

Peer Pressure Induces Biofilm Production. Biofilm formation, cannibalism… anything to postpone sporulation. Marvin Friedman explains.

What’s the Score on the Microbiome? (Elio) Is the human intestinal microbiome a good thing or a bad one? We kept score for a little while.

Green Flypaper. (Merry) Social spiders use yeast to attract more flies to their web. This strategy works so well than local people bring the webs into their homes to act as flypaper.

One If by Land and Two If by Sea. Marvin tells us how bacteria abandoned the oceans and wandered on land, genome-wise.

Source.

Function and Structure

Pushing the Thermodynamic Envelope into the Proteomic Edge. Why is the temperature for maximum growth rate of bacteria so close to the one at which they die? Graduate student Tracey McDole explains this in terms of entropy, enthalpy, molecular crowding, and other goodies.

Microtubules in the Verrucomicrobial Closet. Once again, cryo-electrontomography comes to the rescue, here revealing the existence of tubulin-containing filaments in a prosthecate bacterium. Daniel Haeusser explains

The Three Faces of Thiomargarita. (Merry) Sulfur-oxidizing Thiomargarita may form clusters or chains or live as sessile cells with a complex life cycle, and all three ‘faces’ of these “sulfur pearls” are beautiful.

Polar Enchantment. (Elio) How to isolate proteins that prefer to be at the poles of bacteria, thanks to a clever technique from the Kevin Young lab.

If It Walks Like DNA, and Talks Like DNA… (Merry) Both plasmids and phages have mastered the art of making proteins that mimic DNA, thus confusing host restriction endonucleases that would otherwise destroy their incoming DNA.

Living On the Edge…of the swarm. Gemma Reguera describes tricky aspects of the physics of bacteria swarming on agar.

Cell Division Through DNA Curtains. FtsK is a somewhat mysterious protein that couples chromosome replication with segregation. Gemma introduces a clever single-molecule technique that allows one to visualize FtsK’s gymnastics. 

Bacterial diversity of cell phones and shoes. Source.

Microbial diversity

Fine Reading: Houses Made by Protists. (Elio) Single cell architects make stunningly large and complex structures for protection.

Ovobacter propellens, Not Your Average Boring Bacterium. (Elio) The fastest known swimmer among bacteria, this poor fellow has not received its due attention.

Pathogenesis

Salmonella’s Exclusive Intestinal Restaurant. (Elio) Salmonella has a unique skill: it can use tetrathionate as an electron acceptor. It’s also pretty good at oxidizing an abundant i substrate in the gut, ethanolamine.

Are Phages the Answer? Given that more ways of fighting bacterial pathogens are needed, the old idea of using phages reemerges, thanks to both Pseudomonas biofilms and a mouse study, as discussed by Marvin.

Fine Reading: Autophagy & the Cytoskeleton. (Elio) Escaping into the cytoplasm of host cells is a device used by some bacteria to avoid autophagy. The host cells respond by coating the bacteria with a protein called septin, which makes them autophagiable.

TB or not TB? Graduate students Jaime Zlamal, Andy Cutting, and Steven Quistad describe the asymmetric cell division of mycobacteria and why this may matter with regard to therapy.

What Happened to Our Friendly Enterococci? (Merry) Pathogens can gain by losing their CRISPR loci, as this makes it easier to pick up plasmids and other mobile elements bringing antibiotic resistance factors.

Source.

Evolution and Genetics

Oddly Microbial. Marcia Stone reviews a book by Michael Yarus, Life From an RNA World, with emphasis on ribocytes, those elusive early cells postulated to have existed “way back.”

The Bacterial Resistome is Both Ancient and Surprising. Marvin tells us that bacteria from caves that have been isolated for eons possess antibiotic resistance genes, including resistance against our new drugs.

How to Reform a Resistant Bacterium. (Merry) Picture this strategy: use temperate phages to deliver dominant antibiotic sensitivity genes into antibiotic resistant pathogens. These researchers offer this as a way to reduce antibiotic-resistant nosocomial infections in hospitals. 

Fine Reading: Nematodes & HGT. (Elio) Nematodes are good at acquiring bacterial genes. Horizontal gene transfer across domains?

Sex to the Rescue. (Elio) Hyperthermophilic archaea, when treated with DNA-damaging UV radiation, sprout pili and make cell aggregates that promote recombination between cells.

On Retrons. Habib Maroon introduces us to features of these mysterious prokaryotic retroelements, also known as multicopy single-stranded DNA/RNA hybrid molecules.

Fine Reading: Small Wonders. Merry offers a fine review by McCutcheon and Moran on why and how bacterial endosymbionts end up with such puny genomes.

Miscellanea

What Is This Link to Mushrooms in Works of Art? Well, that’s one of Elio’s interests. He thinks one can learn about the connection between people and mushrooms by looking at paintings.

Where Mathematicians & Biologists Meet. Biomathematician Joe Mahaffy enlightens us about the distinguished historical connection between biology and mathematics.

The Two Quantitative Steps in the Biology Growth Curve. (Elio) Biology has been invaded twice by physicists and mathematicians in the last several decades. The first wave led to the advent of molecular biology, the second (now) to a lot of useful model making.