Small Things Considered

The Lyme Disease Spirochete Feasts on Tick Antifreeze

This article is lightly modified from one published in the blog Spirochetes Unwound by Microbe Fan. With kind permission of the author.

by Microbe Fan

The deer tick, Ixodes scapularis. Photo: Scott Bauer, USDA
Agricultural Research Service, Bugwood.org. Source.

In the northeastern United States the Lyme disease spirochete Borrelia burgdorferi spreads from one white-footed mouse to another by hitching a ride in the deer tick Ixodes scapularis. Transmission between tick and mouse occurs during the tick's rare blood meals. The larval tick acquires B. burgdorferi from an infected mouse during a blood meal late in the summer, and the spirochetes take up shelter in the tick's midgut. Later the larva molts into a nymph, which then completes the transmission cycle by feeding on an uninfected mouse during the next spring or early summer.

Although blood is potentially a rich source of nutrients for both tick and spirochete, the cells lining the tick's gut rapidly engulf the nutrients, including glucose, an energy-rich sugar favored by B. burgdorferi. The spirochetes must therefore rely on other energy sources if they are to survive the many months between tick feedings. How does B. burgdorferi fuel its survival during this period?

The Microbial Weltanschauung*

by Elio

A bunch of bacteria or a starry night? Source.

Had we been asked some 30 years ago how many prokaryotic cells exist on this planet, the answer would have been perhaps 10²⁰. We might have arrived at such a figure based on an estimate of the total weight of vertebrate turds produced every day and the assumption that they are laden with bacteria. Something like that. We knew that prokaryotes could be found elsewhere, but had no idea about their number. We thought that the oceans or soils were not all that rich in prokaryotic life. That was logical enough, given the non-culturability of the majority of prokaryotes isolated from natural environments and the adherence to the idea that “if you can't culture it, it doesn’t exist.”

When proper body counts began to be made, usually via fluorescence microscopy, the numbers jumped upwards by at least 10 orders of magnitude to over 10³⁰. We now know that bacteria comprise about half the biomass on this planet, a stunning realization. This is not just a numbers game: it is a fundamental shift in how we perceive life on this planet. Suddenly, participation of the prokaryotic cells in the chemical and physical transactions of this planet has taken center stage. Microbes are directly involved in the exchanges of matter via biogeochemical cycles, in shaping the geological landscape, and even in altering the weather. Although some suspected such crucial roles for microbes, such fanciful notions were generally discounted until the new numbers appeared in our consciousness.

Phage Lambda’s Polar Expedition

Localization by direct fluores-
cence microscopy of the GFP–
ManY fusion in E. coli. Arrows
= foci at the poles; arrowhead
= focus at mid-cell. Source.

by Merry

For a long, long time, phage lambda (λ) has known that its E. coli host was not simply ‘a well-stirred bag of enzymes’ (something we’ve come to appreciate only relatively recently). This is vital information for lambda since it needs to interact with two particular host proteins in order to launch an infection. One is its receptor (LamB) located on the outer membrane (OM), the other is an inner membrane protein, ManY.

ManY works for E. coli as part of the inner membrane mannose transporter, whereas for lambda it is required for entry of the phage’s DNA into the cell. And ManY is not part of that imaginary stirred gemisch. Using a ManY-GFP fusion protein and fluorescence microscopy, Edgar and colleagues demonstrated that ManY is localized at the cell poles and at cell division sites (future cell poles) in living cells.

They also found that at low MOI (a Multiplicity Of Infection of 0.5–5) lambda, too, prefers the polar regions, ‘binding’ preferentially at the poles and future poles (mid-cell). (This ‘binding’ is not the initial adsorption which does not require ManY, but rather is irreversible binding visualized after incubation periods of up to an hour, followed by pelleting of the cells by centrifugation.) This they visualized using phages labeled with tiny QDots (10-20 nm in size versus lambda’s ~60 nm diameter capsid and ~150 nm long tail) that do not interfere with infection.

They repeated these experiments using five other coliphages, some temperate and some lytic, as well as two other phages that infect other Gram-negative hosts (Yersinia pseudotuberculosis and Vibrio cholerae). All showed the same pattern of polar localization.

Bacteria Living Without Phages?

by Merry

Are there environments where there are abundant bacteria and no phages? Sounds like one of our Talmudic Questions, but this one has a specific answer, and that answer is Yes. That environment was found within a cystic fibrosis (CF) lung.

This story comes from a pair of papers recently published by a group of microbial ecologists reporting their survey of the microbes and DNA viruses present in the lungs of two late-stage CF patients. Previous studies had all relied on sampled sputum or bronchial alveolar lavage fluid. These researchers instead took advantage of the opportunity to investigate the explant lungs from a CF patient who received a lung transplant. They dissected the lungs, isolated the microbes and viruses separately from each lobe, and then extracted the DNA. This approach enabled them to determine not only the diversity within each lobe, but also to ask whether each lobe housed its own distinctive community.

The Façade of E. coli K-12

by Elio

A good source of information on the
history of the recombinant DNA
controversy by the then-director
of the NIH. Source.

In the early days of recombinant DNA research (ca. 1973), a thunderous debate took place regarding the safety of genetic engineering. On the one side were those who proposed that messing with the genome could lead to the emergence of novel and potentially pernicious pathogens. On the other side were those who reasoned that the resulting organisms were unlikely to be more virulent than those already in existence. The history of that era has been recounted many times. (For links to some accounts, click here.) Central to the arguments was the conviction that the most popular organism used for cloning, E. coli strain K-12, was unquestionably a non-pathogen. Sure enough, human volunteers who drank cultures of K-12 did not become colonized and walked away with no untoward effects. Throughout the arguments that ensued, confidence in the benevolence of K-12 remained unbroken.

This longstanding article of faith has now been shaken. A report from the laboratories of S. Kar in New Delhi and S. Adhya at the NIH alerts us to the fact that the K-12 strain is not as benign as we thought. It has been known for some time that the abundant noninvasive strains of E. coli in our microbiota carry cryptic (i.e., unexpressed) genes for virulence factors. The news here is that these genes are activated by a mutation in a protein called HU, a small, basic, DNA-binding protein. HU is the most abundant of the so-called nucleoid-associated histone-like proteins of E. coli that are involved in maintaining the structure of the nucleoid. By controlling DNA superhelicity, HU regulates many processes, including gene expression, DNA repair, and the initiation of chromosome replication. Therefore, mutations in HU are, of necessity, pleiotropic, affecting many cellular functions. In E. coli, these mutants usually have a mild phenotype due to the presence of other proteins with analogous properties. Although many HU mutants grow at rates comparable to the wild type, some show defects in cell division and response to temperature or UV shocks.

There is Hope

by Elio

Through the years, we have not had many opportunities to look forwards, to get a feeling for how science is taught in middle and high schools. But we have had a couple of wonderful encounters, one with the Jefferson Middle School and Mrs. Putnam, their sixth grade teacher in Jackson, Mississippi. Their blog, Science is a Blast is well worth visiting, which is an understatement. The number of great links alone is worth the price! We’re glad that this blog is somewhere among the ones offered to the students.

Source.

The second of our past contacts is a blog called Extreme Biology, maintained by teacher Stacy Baker at Calverton School in Huntington Maryland. This blog, notable for its depth and breadth, won the 2008 Edublog Award for Best Class Blog. And MS. Baker was prominently featured in an episode of NPR’s Science Friday. One of her students wrote a story about how wood can be treated with fungi to produce Stradivarius-grade violins based on something we had written here.

Not knowing much about the state of education in this country, we are chary of commenting on the current state of affairs. However it is clear from our brief contact with youngsters and from other anecdotal indications that at some of the best teaching is very good indeed. Let’s hope it spreads further.

What’s Old is New: Genome Wide Manipulation of the Bacterial Chromosome in Vivo

by Michael G. Schmidt

Every now and then you come across an article that makes you sit back and hear yourself say Wow! This is what happened to me recently while preparing to discuss a paper on This Week in Microbiology (TWiM), a bi-weekly podcast produced by Vincent Racaniello and ASM, or as I think of it, a journal club open to any who are curious about all aspects of microbiology. The paper by Church and colleagues, published in Science, describes the precise manipulation of bacterial chromosomal sequences on a genome-wide scale. Titles matter, and this one, Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement, spoke volumes. Before even reading the abstract, it caused me to ask, Have these authors found the Holy Grail that synthetic biologists have been searching for? I’ll let you be the judge as I take you through the world of Multiplex Automated Genome Engineering (MAGE) and Conjugative Assembly Genome Engineering (CAGE).

Here's what they did: they replaced all of the 314 TAG amber stop codons, scattered across the 4.6 megabase genome of Escherichia coli with the synonymous TAA ochre codon. This means that they would then have strains with a free codon that can be reprogrammed to do other things. You might be asking, What things? This really is a subject for another STC piece on cellular engineering written from the perspective of a synthetic biologist. But, in keeping with the theme of What’s Old Is New, one could envision the alteration of a tRNA gene, sneaking it into the chromosome via a limited version of MAGE, such that its product will now recognize the TAG codon and substitute a novel or unique amino acid into a protein resulting in the desired/engineered phenotype. Mother nature has already provided the proof of concept: extragenic suppression of existing amber mutations.

Talmudic Question #80

Within the microbial world, is the degree of pleiotropy displayed by an organism inversely related to its genome size?

Shipwreck Microbiology

by Merry

Millennium Atoll (formerly Caroline Island) is one of
the Southern Line Islands located in the central Pacific
approximately 1500 km south of the Hawaiian Islands.
Photo credit: Jennifer Smith.

The coral reef at uninhabited Millennium Atoll (formerly Caroline Island) in the central Pacific is one of the few near-pristine reefs remaining in the world. By good fortune, Millennium has avoided most of the local devastation that has befallen other atolls in the Line Islands through colonization, extensive fishing, and ‘improvement’ for use as military air strips or nuclear test sites. The reef is teeming with fish, including apex predators; the benthos has high coral cover; the water is crystal clear.

Most of the reef, that is. The scene is different in the vicinity of the wreckage from the 85 ft steel tug that ran aground in 1993. Here the water is murky and the colorful corals are replaced by macroalgae, cyanobacterial mats, and corallimorphs  (a cnidarian, similar in structure to corals but lacking a skeleton). Combined this gives the sea bottom a dark, foreboding look. There are four more of these ‘black reefs’ on other atolls in the region, all associated with shipwrecks. They can develop quickly, within three years, and persist for at least decades. Correlation, however, does not prove causation. So a group of microbial ecologists, appalled by what was happening, set out to track down the connection between these shipwrecks and the black reefs. Some potential suspects, such as copper paint and petroleum products, could be immediately eliminated because they were not common to all five wrecks.