Bacteria

Carl Zimmer offers a quick look at an alternative theory being put forward by James Lake, a University of California - LA researcher, concerning the origins of complex cells in early life forms. First a bit of background from Zimmer:

We are, fundamentally, a fusion. As I wrote in my essay for Science on the origin of eukaryotes, there's now a wealth of evidence that our cells evolved from the combination of two different microbes. The mitochondria that generate fuel for our cells started out as free-living bacteria. Today, they still retain traces of their origin in the bacterial DNA they carry, as well as their bacterial structure, including the membrane within a membrane that envelops them.

Scientists I spoke with as I worked on the essay agreed that this merging was a profound event in the history of life. No living eukaryote, whether animal, plant, fungus, or protozoan, has completely lost its mitochondria since that symbiotic milestone some 2 billion years ago. It wasn't the only time that two species merged, however. Plants, for example, descend from algae that engulfed a species of photosynthesizing bacteria. Many protozoans have swallowed up photosynthetic partners as well.

Yet in all these cases, eukaryotes did the swallowing. It's striking that scientists have such a hard time finding an example of a noneukaryote (a prokaryote such as Escherichia coli and other bacteria) hosting a prokaryote symbiont. Some scientists have gone so far as to argue that swallowing up a partner requires lots of intricate molecular systems that can create a pocket in the surface of a cell and can draw that pocket inside the cell as a bubble. Eukaryotes have this sort of cellular skeleton, and prokaryotes, it seems, don't. If that's true, then our ancestors swallowed up mitochondria only after they evolved the molecules necessary for the swallowing.

I'm fascinated by the symbiotic mergers of two or more life forms to create new life forms or enhance existing ones. Studies of Mitochondria have delivered some of the strongest evidence that this has occurred, leaving a natural history of symbiotic interaction in most eukaryotic cells. Mitochondria possess their own DNA which is only passed down through maternal inheritance (from the female in each species). I imagine that differences in mitochondria found in various species alone could occupy the careers of myriads of cell biologists. For example:

In animals the mitochondrial genome is typically a single circular chromosome that is approximately 16-kb long and has 37 genes. The genes while highly conserved may vary in location. Curiously this pattern is not found in the human body louse (Pediculus humanus). Instead this mitochondrial genome is arranged in 18 minicircular chromosomes each of which is 3–4 kb long and has one to three genes. This pattern is also found in other sucking lice but not in chewing lice. Recombination has been shown to occur between the minichromosomes. The reason for this difference is not known.

Anyway, the meat of Zimmer's post:

But today, there's a provocative new alternative to consider. Maybe a lot of today's prokaryotes are also the result of an ancient merger. The idea comes from James Lake of the University of California, Los Angeles, a veteran researcher on the early history of life. In my essay, I describe how Lake first proposed in the early 1980s that the host cell that gave rise to eukaryotes belonged to a lineage of prokaryotes he dubbed eocytes. Now, a quarter of a century later, new studies on genomes are strongly supporting his eocyte hypothesis. In today's issue of Nature, Lake questions whether we may be too quick to assume that only eukaryotes are the result of fusion. He observes that aphids depend on a species of bacterium called Buchnera to digest their food, and Buchnera in turn contains other bacteria on which its own survival depends. These two bacteria are still distinct enough from each other that we can tell them apart. But what if two bacteria joined together billions of years ago and their identities blurred together? How would we tell them apart?

To look for possible signs of ancient fusion, Lake compared proteins in over 3000 different prokaryote genomes. He concluded that a major group of bacteria known as Gram-negative bacteria is actually the result of a fusion of two different kinds of bacteria, known as Actinobacteria and Clostridia. These bacteria, which include the ancestors of mitochondria, are unusual in many ways, but the most obvious one is their membranes. Whereas other bacteria are surrounded by a single membrane, Gram-negative bacteria are surrounded by two. It's possible, Lake argues, that the double-membrane structure of these bacteria is a vestige of one kind of bacteria living inside another.

(...) genetic engineers have developed a new technique known as MAGE – multiplex automated genome engineering. What they do is to essentially evolve bacteria with optimized or at least greatly improved production of the substance of interest. The technique causes bacteria to rapidly mutate – causing thousands of mutations and billions of different strains. (...)

The MAGE technique is also interesting because it is a direct application of evolutionary principles. The process works by increasing diversity randomly through mutations and then selecting those bacteria that by chance have the desirable trait. This clearly demonstrates that the two step process of evolution – random diversity and selection – works.

Creationists have argued that evolution cannot work because random mutation cannot provide specificity and direction, and that selection cannot increase information because it is a negative process – it only removes information. This argument is nothing but a diversion from logic and reality, however. It should be obvious that mutations increase information and selection provides non-random specificity and direction.

In response to MAGE as an example of evolutionary principles, creationists are likely to argue that the MAGE technique allows for the inclusion of genetic mutations already known to be desirable into the mix – including introducing genes from other species. So the diversity does not have to be entirely random. But even when it is, the process still works. Also, the selection is artifical, not natural. This is an old objection by creationists to artifical selection as an anology of evolution. This is a non sequitur, however – the analogy is that selection can drive non-random change in a randomly varying system. It doesn’t matter if the selection is artificial or natural, all that matters is differential survival.

By itself, of course, MAGE does not prove that evolution is true. No single line of evidence can do this. But is does support basic evolutionary principles with a practical application. Creationists often charge that evolution has no practical application, as if utility is a marker of scientific truth. Not only is this argument fallacious, it is factually incorrect. Creationists excel at being wrong in two or more ways simultaneously. At least they are good at something.

Scientists programmed the E. coli to count by injecting them with a molecule containing two DNA sequences that behave like switches. One switch turns on a minute-counter. The other switch turns on an hour-counter.

The first switch turns on proteins that physically flip a piece of RNA when the E. coli are exposed to sugar over the course of several minutes.

The second switch turns on proteins that flip a small section of DNA over the course of 10 to 15 hours in response to alternating periods of light and dark.

Both switches can flip only three times -- or count to three. Once they reach that number the DNA switches turn on another engineered protein, called a green fluorescent protein, or GFP, which glows green and lets the scientists know that their bacterial timers worked.

This function allows scientists to detect as bacteria count up -- 1, 2, 3, etc. So, the cells could be used to count the number of times it encounters a particular toxin or drug.

Discovery News let us know about a story in the new Science about a spectacular find below the Antarctic glaciers:

It's a particularly tough environment, with no light, no oxygen, and extremely cold temperatures. But the microbes appear to live -- and thrive -- off a combination of iron and sulfur, according to a new study. The result of that strange metabolism is a brilliant red streak of cascading ice called Blood Falls.
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The chemical analyses showed that the microbes breathe in a form of iron that leaches into the water from the bedrock below. Then, with the help of sulfur compounds as catalysts, the microorganisms breathe out a different form of iron, which gives Blood Falls its rusty color.

This is an excellent presentation given by microbiologist Bonnie Bassler at TED talks. She explains how biologists have discovered chemical language used by bacteria to dictate behavior and analyze their neighbors. Fascinating subject.