Small Things Considered

TWiM #40: A Mecca for Microbiology

Hosts:  Vincent Racaniello, Stanley Maloy, Waclaw Szybalski, and John Kirby

Vincent and Stanley meet with Waclaw Szybalski and John Kirby at Cold Spring Harbor Laboratory on the occasion of its designation as a Milestones in Microbiology site. They reminisce about how the well known laboratory has advanced the science and teaching of microbiology, and discuss John’s work on the soil dwelling, predatory myxobacteria.

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Links for this episode:

• Cold Spring Harbor Laboratory
• Milestones in Microbiology
• Bacteria, Archaea, and Phages meeting at Cold Spring Harbor
• A bacterial wolfpack (FEMS Micrbiol Rev)

Send your microbiology questions and comments (email or mp3 file) to twim@twiv.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twim.

Revisiting BYOG: Bring Your Own Gene

by Merry Youle

This image, that accompanied the original BYOG
post, is a 17th century illustration of the Copernican
model of a heliocentric universe. Source.

For this, my last post as co-blogger, I chose to loop back to my very first post about my favorites among the many Small Things, the phages. That was BYOG: Bring Your Own Gene, published in March of 2008, recounting what was at the time a totally new story for me. Amazing! Those ingenious cyanophages brought along genes to keep the energy flowing for phage replication by maintaining active photosynthesis in their doomed cyanobacterial host.

The story back then was rather straightforward. The focus was on the genes that encode the two proteins at the core of photosystem II, D1, and D2, both proteins being subjected to photodamage. D1 in particular has an especially high turnover rate. The notion was that when the phage shuts down host protein synthesis, damaged D1 would not be replaced, photosynthesis would decline, and this would impact phage replication. Made sense.

Indeed, it was a good story. It had begun back in 2003 with the first report of photosynthesis genes encoded by a phage. That was followed in 2005 by a paper showing that these genes are actually expressed and translated into proteins during infection. By 2007 more such “host genes” had been identified in various phage genomes. Increasingly it was realized that these genes, though not essential for phage replication in the lab, provided fitness benefits to the phage. They were given the name auxiliary metabolic genes (with the acronym AMG). Since then, the array of AMGs has grown and includes genes involved in phosphate acquisition, nucleotide metabolism, and cytoskeletal construction (soon to be discussed on STC), as well as numerous genes involved in photosynthesis.

The Road to Microbial Endocrinology

Stress. Source.

by Mark Lyte

The emergence of the field of microbial endocrinology did not follow a straight course, nor was the destination intuitively obvious at the start. Like many research paths before it, the theoretical underpinnings of the field only emerged when it became obvious that the only explanation for the facts was a new awareness, in this case the realization that microorganisms are more interactive with the host than previously recognized.

The development of microbial endocrinology, the intersection of microbiology and neurophysiology, has its roots in the field of stress research. In the 1980’s, there was growing recognition that host neurophysiology, specifically the elaboration and production of a panoply of various neuroendocrine hormones/neurotransmitters, modulated certain immunological phenomena. For example, the stress-related family of neurohormones, the catecholamines, could influence the production of antibodies against specific antigens. The direct interaction of neuroendocrine hormones on immune cell function was being examined from a mechanistic standpoint (i.e. direct examination of hormones and immune cells in an in vitro system). But beyond that it became apparent that the nervous system as a whole regulates immunity. The involvement of the brain and associated systems in the direct control of immune responsiveness was led by Ader and Cohen who established the field of psychoneuroimmunology [1]. It was in this field that I found myself as a newly-minted assistant professor with my first NIH grant.

Requiem for a Machine

by Elio

Beckman analytical ultracentrifuges, then (the Model E)...

Here’s a challenge for present-day systems biologists. Say you wanted to find out how many ribosomes are present in cells growing under different conditions. How would you do it? You might think of using quantitative PCR to measure the amount of rRNA inside the cell. However, you could end up with an overestimate because some of the rRNA may not yet be assembled in mature ribosomes. For instance, add chloramphenicol, a protein synthesis-inhibiting antibiotic, to a culture and you will measure increases in the cellular levels of rRNA due to the accumulation of non-functional, immature ribosomes. Perhaps, then, you would roll up your sleeves and run a sucrose gradient to separate the mature ribosomes from their precursors and immature forms by size fractionation, but this is a labor intensive method that not many people like to do these days. We’ll agree that making such measurements may not be as easy as it sounds. So let me reminisce about how we carried this out in the old days. All it took was a fancy apparatus and some chutzpah.

Life On the Edge: What Happens When Phosphorus Is Limiting?

by Howard Goldfine

Schematic drawing of a lipid bilayer. Source.

For many bacteria, scarcity of phosphorus—serious though it may sound—is not insurmountable. True, phosphorus is needed for nucleic acids and phospholipids, but many prokaryotes have found a way to reduce their need of this element for phospholipid synthesis. But first, why are there phospholipids in the first place? In these compounds the phosphate links the glycerol lipid backbone to a polar “head group” that possesses a free hydroxyl group. In bacteria, the most common head groups contain ethanolamine, glycerol, or, less frequently, serine or choline (Fig. 1). These polar ends can interact with water or with each other, while the hydrocarbon tails interact with each other to form the lipid bilayer. Provided with such amphipathic constituents, a cell can surround the rest of the cell machinery with a semipermeable membrane containing proteins embedded for various functions.

But what happens when phosphorus is in short supply, as it is in the oceans and some inland environments? The cells still need lipids with polar head groups. Bacteria have evolved a number of clever (some may say fiendishly clever) ways to nevertheless make membranes without phosphorus. Let me divide these strategies into two groups, those that use sugars and those that use an amino acid or parts thereof.

TWiM #39: What Darwin Never Knew

Hosts: Vincent Racaniello, Michael Schmidt and Elio Schaechter

Vincent, Michael, and Elio review chapters from Microbes and Evolution, a collection of short, personal essays by microbiologists.

Click to play current episode
Or right click to download file. (55 MB .mp3, 75.5 minutes)

Subscribe to TWiM (free) on iTunes, Zune Marketplace, via RSS feed, by email or listen on your mobile device with the Microbeworld app.

Links for this episode:

• Azam Lab
• Europa (Wikipedia)
• First marine viral metagenomic analysis (PNAS)
• Phage-encoded toxin genes in SoCal waters
• Bacterial photosynthesis genes in a virus (Nature)
• Forest Rohwer on MicrobeWorld Video
• DNA replication fidelity (J Biol Chem)
• Replica plating (Wikipedia)
• Letters read on TWiM 039

Send your microbiology questions and comments (email or mp3 file) to twim@twiv.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twim.

Fine Reading: Speciation by Symbiosis

by Elio

The parallel relations between a phylogeny of insect species based on mitochondrial genes (the parasitoid species Nasonia and their host fly (Sarcophaga bullata) and a dendrogram of the microbial community relations based on a bacterial gene. Note the close correspondence between the phylogeny of the two lineages. Source.

No doubt, one of the defining events in evolution was the acquisition by some primitive cell of bacterial symbionts that became mitochondria and chloroplasts. Symbiosis has, in fact, driven evolution in many other ways and has had a profound effect in the origin of species. For a deeper understanding of how symbioses has affected speciation, a pertinent review by R. M. Brucker and S. Bordenstein is well worth reading. Based on their own research with the insect endosymbiont Wolbachia, the authors describe how symbiosis affects the reproduction of the insect hosts and, ultimately, the fitness of the species. As the authors point out, there is complementary arithmetic in this relationship: symbiosis makes two organisms into one; speciation, one into two!

Some of the examples they cite are startling. For one, Wolbachia, like some other bacterial symbionts of insects, induces parthenogenesis in the insect host, a form of asexual reproduction that does not involve fertilization and leads to what is called “asexual speciation”. Click here and here for some of our previous posts on Wolbachia. For another, Drosophila flies reared on different diets house different microbiota, and show strong mating discrimination; ergo, the symbionts dictate who mates with whom. Further, bacterial symbionts that we could classify as vertically-transmitted, nutritional mutualists (e.g., insect symbionts in the genus Buchnera) assist in resource exploitation, thereby creating new ecological opportunities for their host. In some cases, host and endosymbiont appear to have evolved together. There is even more. Endosymbionts can also induce cytoplasmic incompatibility.  Here the offspring of infected males and uninfected females are sterile, therefore, unproductive. In other cases, the offspring of hybrid matings become more susceptible to infection than non-hybrids, which may reduce their fertility and viability. How all of these examples of symbioses affect speciation is discussed in detail in the article.

MicroRNAs and Retroviral Integrity

The tumor shown here was caused by bovine leukemia
virus (BLV). BLV’s mechanism of tumorigenesis has
long been a mystery, but researchers have recently
discovered a virus-encoded miRNA that may be the
culprit. Source.

by Jamie Henzy

Among retroviruses, the deltaretrovirus genus is something of a shady bunch, its members lurking in the shadows, causing trouble in the form of persistent infections that result in lymphomas and leukemias. At this time, we know of no endogenous sequences that might be their ancestors—the lone retroviral genus (of seven) for which this is the case, as if they’ve intentionally covered their tracks to elude the authorities. Fittingly, two members of this clan are emerging as particularly resourceful and crafty, exposing novel tricks in the viral arsenal.

These two are bovine leukemia virus (BLV), which infects cattle and causes B-cell tumors, and human T-lymphocytic virus (HTLV)-1, which causes T-cell tumors in its human hosts. Merry blogged about the stealth method of cell-to-cell spread employed by HTLV-1—how it uses immunological synapses to directly access target cells and avoid the exposure to immune defenses that a free virus particle would face. Not to be outdone by its sly associate, BLV has recently won the honor of being the first RNA virus convincingly shown to encode microRNAs.

Ehux: The Little Eukaryote with a Big History

by Jaime E. Zlamal

Coccolithovirus, a giant double-stranded
DNA virus, infects Ehux. The virus (pink)
was first observed in 1999 by W.H. Wilson
and was found to be a “giant-virus” having
472 protein-coding genes. Source.

There is an organism out there that is smaller than you, older than you, and that has a house that’s probably fancier than yours. Meet Emiliania huxleyi, or Ehux. Ehux is a miniscule coccolithophore, a beautiful single-celled alga that doesn’t get enough attention in the world of microbiology. The tendency of biologists to ignore this phytoplankton species belies its significance. In fact, Ehux has a penchant for being flashy—it has phenomenally beautiful plates covering it, known as coccoliths, intricate composites of calcium carbonate that when viewed under the microscope rival the most wondrous sculptures made by man. And they exist in huge quantities. The White Cliffs of Dover wouldn’t be so large, or for that matter, white, if it weren’t for this tiny architect. Ehux makes blooms near the surface of the oceans that are so big they can be seen from space! And it has its own web page.

Two Tales of Symbiosis

by Elio

Immunogold staining of the ovary of the tick Ixodes
ricinus using antibodies against the major flagellar
protein, FliD. Arrows indicate the gold particles present
on the surface and inside bacteria-like structures. Source.

I don't get tired of symbioses, something I attribute to the Power Law of Symbiosis I just made up: Interacting genomes are more interesting than single ones by the n^th power of their numbers, where n is a matter of personal preference. Here I relate two examples that should make the point.

My first story is about a finding that should have caused its Italian researchers to use a mild expletive, such as “Corpo di Bacco!” (“By the body of Bacchus!” I grew up in Italy, which entitles me to this bit of linguistic irrelevancy.) What they found is amazing. That a bacterial endosymbiont had been found to dwell inside the mitochondria of ticks was surprising in itself (see a previous post), but to now find them to possess what looks to be a complete set of flagellar genes, twenty-six in number, is stunning. First, do these genes actually work, that is, actually produce flagella? Convincing proof of that is still lacking because, as the authors point out, observing flagella in electron microscope sections is not easy; they are very hard to distinguish when cut crosswise. However, these genes are transcribed and one of their products can be identified on the surface of the endosymbionts. In addition, these genes have conserved domains and structural features typical of other flagellar genes.