Bacteria as Antibiotics

Researchers at the University of Virginia have decoded the genome of a type of bacteria,  Micavibrio aeruginosavorus, that can survive by attaching to another bacterium and “essentially” sucking out its nutrients, killing its prey in the process. If it can be made to target the right pathogenic bacteria in our bodies, this could be used as an antibiotic in the future.

From PhysOrg:

The bacterium, Micavibrio aeruginosavorus, was discovered to inhabit wastewater nearly 30 years ago, but has not been extensively studied because it is difficult to culture and investigate using traditional microbiology techniques…

The bacterium “makes its living” by seeking out prey – certain other bacteria – and then attaching itself to its victim’s cell wall and essentially sucking out nutrients. Unlike most other bacteria, which draw nutrients from their surroundings, M. aeruginosavorus can survive and propagate only by drawing its nutrition from specific prey bacteria. This kills the prey – making it a potentially powerful agent for destroying pathogens.

One bacterium it targets is Pseudomonas aeruginosa, which is a chief cause of serious lung infections in cystic fibrosis patients…

Additionally, because M. aeruginosavorus is so selective a feeder, it is harmless to the thousands of beneficial bacteria that dwell in the general environment and in the human body…

Another benefit of the bacterium is its ability to swim through viscous fluids, such as mucus. P. aeruginosa, the bacterium that colonizes the lungs of cystic fibrosis patients, creates a glue-like biofilm, enhancing its resistance to traditional antibiotics. Wu noted that the living cells of M. aeruginosavorus can swim through mucus and biofilm and attack P. aeruginosa.

M. aeruginosavorus also might have industrial uses, such as reducing bacteria that form biofilms in piping, and for medical devices, such as implants that are susceptible to the formation of biofilms.

This is a pretty interesting idea to me. One would hope that we could engineer M. aeruginosavorus to hunt down very specific pathogenic bacteria, but there’s definitely a potential danger of accidentally killing beneficial bacteria in our bodies and producing nasty side effects. They don’t say at all how M. aeruginosavorus works, but another potential issue is that some individual bacteria will be resistant to its attack, and bacteria populations will develop resistance to it just like any other drug. 

In any case, the more potential pathogen-killers the merrier, so I’m interested to see where this research goes in the future.

Edit: PhysOrg accidentally called Pseudomonas aeruginosa “Pseudomonas aeruginosavorus“, seemingly mixing it up with M. aeruginosavorus, so I edited the quote above for accuracy. Many thanks to johan for pointing that out. 

A Microbe Census Deep in the Earth

There are lots of microorganisms out there; we’ve only identified a fraction of them. Just as the deep dark oceans represent a huge question mark in terms of the incredible amount of undiscovered species, the subterranean offers a daunting opportunity to discover new forms of life. A new census, called the Census of Deep Life, is determined to find and categorize microorganisms living 10 to 100 kilometres below the Earth’s crust. 

A microbe, or microorganism, is just an organism that you can only see under a microscope. They’re usually unicellular. Bacteria are the most prominent example, but there are others across the spectrum, like algae (various kingdoms), slime molds (protist), yeast (fungus), dust mites (animal), and even single-celled plants

From LiveScience:

Little research has been done to identify the unicellular denizens of the Earth’s inhospitable depths. An ocean microbe census indicated that as many as a billion kinds of microorganisms live in the planet’s seas, but the deep Earth is more difficult to access, and microbial populations are more sparsely distributed.

Yet the data that are available on crust-dwelling species suggest that as many as several million categories of bacteria and their unicellular relations could live in the planet’s deeps…

For the census-takers of microbes, it’s a huge challenge to identify distinct species.

“Microbiologists have tried to do so the way traditional biologists have, but they’re frustrated by this because microorganisms tend to trade DNA,” Colwell said. In fact, microbes can swap DNA by merely engaging in what amounts to hand-holding.

Such a cavalier exchange of genetic material makes it difficult to unequivocally differentiate one group of microorganisms from another.

However, the microbe census is focused on getting samples from deep, isolated communities that have been left to their own evolutionary devices for long periods of time, and may have distinctive genetic characteristics.

The project receives rock and fluid samples retrieved from diverse environments such as caves, mines, and drill projects on land, and from projects in the ocean that have drilled deep beneath the seafloor.

Finding very unique species would be awesome. For example, a very important protein used in labs for DNA replication was taken from bacteria that were discovered in hot springs at 70°C. The protein is useful because of its resistance to heat, and is key to conducting modern molecular biology research. Who knows how discovering novel kinds of life could change science in the future?

On a separate note, I probably won’t be posting anything tomorrow (unless I really need a break) because I have my GRE biochemistry test on Saturday morning, and I have a marathon of cramming to do before then. Afterwards I’ll make up for it with some extra posts though, for your and my entertainment – provided this test doesn’t turn me off of science entirely. 

On the Origins of Viruses

Wired has an interesting article from Ars Technica on the questions raised by recent discoveries of some huge viruses (“huge” relative to other viruses of course). The characterization of viruses themselves challenged biologists’ definition of life, and these giant viruses do so even more. They’re as large as some bacteria, contain genes previously thought to be specific to cells, and one virus (mamavirus) even gets infected by a small virus – the first known virophage, a virus that infects a virus.

This article, though, is about their origins; when did these giant viruses originate, and are they the ancestors or descendants of cellular life?

The unusual size and gene content of the virus led one scientist to suggest that viruses could explain the origin of DNA-based life. If viruses carried all these genes, then it’s possible to imagine that one could set up shop in a cell and simply never leave, gradually taking over the remaining functions once performed by its host’s genetic material. This would explain the origin of DNA, which would distinguish the virus from its host’s genetic material, a holdover from the RNA world. It could also explain the existence of a distinct nucleus within Eukaryotic cells.

Eukaryotic cells (like those found in plants and animals) have a nucleus; prokaryotic cells (like bacteria) do not. The “origin of DNA-based life” is a reference to the fact that it’s theorized that life used to rely on RNA as its chief genetic code, the job DNA does now. And the idea of a virus “setting up shop” in a cell and forming a nucleus is similar to mitochondria and chloroplasts, organelles (cellular compartments) in eukaryotic cells that used to be bacteria, and still have their own DNA and everything. 

A paper is being released today, however, that argues that this scenario has things exactly backwards. Giant viruses, its authors argue, have all these genes normally associated with cells because, in their distant evolutionary past, they were once cells…

And what they find supports the view that the virus started out with a much larger complement of genes… Both viruses share an identical set of genes involved in transcribing their DNA into RNA, and use an identical set of signals to indicate where the transcripts should start and stop…

Clearly, the common genes suggest that the viruses share a common ancestor. This leaves two possibilities for the novel ones: either the ancestral virus had a larger collection and its descendants have lost different ones, or each virus picked up different genes from its hosts through a process called horizontal gene transfer. The authors favor the former explanation, because most of the genes specific to one of the two viruses don’t look like any gene present in their hosts (or any other gene we’ve ever seen, for that matter).

So, when did the common ancestor exist? The authors line up a few of the conserved megavirus genes (including those of a more distantly related giant virus, CroV) with the equivalents in other eukaryotic species, and find that they branch off right at the base of the the eukaryotic lineage. In other words, the viruses seem to have had a common ancestor with eukaryotes, but it split off right after the eukaryotes diverged from bacteria and archaea…

To the authors, this suggests that the viruses are the evolutionary descendants of an ancient, free-living eukaryotic cell. Various genes and structures from that organism have gradually been lost over its long history as a parasite, leaving something that propagates like a virus, but belongs to a distinct lineage from all other viruses that we’re aware of.

The authors make a reasonably compelling case against the megaviruses getting their complex genomes via horizontal gene transfer, although it would be good to see a similar analysis for a lot more of the shared genes. What they don’t do, however, is rule out the initial alternative: it’s still technically possible that the megaviruses and eukaryotes share an ancient common ancestor because all eukaryotes are descendants of the virus’ genome. At the moment, I’m not sure it’s possible to distinguish between these alternative explanations.

If this is true, that would mean we’re more recently related to these viruses than to bacteria or archaea. It’d also imply that a living species evolved into non-life. I bet Darwin wasn’t counting on that.

Parasite Inhibits Your Immune System, Changes Your Behaviour

Via Science Daily: There’s a protozoan parasite called Toxoplasma gondii that can manipulate behaviour; for example, causing rodents to seek out felines, as a means of getting T. gondii to their breeding ground in the feline intestine (here’s a video of a zombie-rat in action). In humans, T. gondii have been linked “to behavioral and personality shifts, schizophrenia and population variations, including cultural differences and skewed sex ratios.” Sounds like powerful stuff. Good thing our baller immune system can destroy it… right?

No 😦 .

These highly contagious protozoa infect more than half the world’s population, and most people’s immune systems never purge the intruders…

“We found that Toxoplasma quiets its host’s alarm system by blocking immune cells from producing certain cytokines, proteins that stimulate inflammation…”

When immune cells meet intruders, they release cytokines that summon more immune cells, which produce more cytokines, rapidly causing inflammation. T. gondii must allow cytokines to trigger enough of an immune response to keep its own numbers in check and ensure host survival. But too many cytokines cause an overwhelming immune response that could damage the host or eliminate the parasites…

“Cells infected with Toxoplasma produced no messages to trigger inflammation,” Denkers said. “Our colleagues at Stanford University found that Toxoplasma produces a specific protein called ROP16 to suppress inflammatory responses. Collaborating with parasitologists at Dartmouth Medical School, we found that Toxoplasma sends ROP16 to infiltrate communication channels in immune cells, causing them to lower cytokine production.

Apparently, this is the first known parasite to wield this superpower. Who knows what other kind of creepy crawlies are lurking inside of us? Now, go off into the world, acting strangely, and intelligently inform people that the T. gondii made you do it.

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