Saturday, May 29, 2010

Friday Fuligo, continued

The “dog barf” phase of Fuligo’s life is like the adult stage of a mayfly’s life. The mayfly larva lives for months as a predator in streams and lakes before spending a single day as a sexually reproducing result. The dog barf also lasts a single spectacular day devoted to reproduction, but it’s the last stage of a much longer predatory life.

Fuligo spends most of its life growing as a weird thing called a plasmodium. The plasmodium starts out as an ordinary eukaryotic cell, something like an amoeba. It’s mobile and predatory, and it engulfs any smaller cells it encounters as it creeps along its way. Unlike an amoeba, or any normal cell, it doesn’t divide as it grows. The cell just gets bigger, and BIGGER, and BIGGER. It copies its DNA, and its nucleus divides, so the result is a plasmodium: an enormous (well, a couple of centimeters) single cell membrane enclosing millions of nuclei. It has been reasonably compared to the title character in the B-movie classic “The Blob,” only instead of terrorizing Steve McQueen, it mows down bacteria and protozoa. If you’re lucky, you can sometimes see a plasmodium, a sort of film growing on moist humus.

When the time is right the Fuligo plasmodium gathers itself up and turns into the beautiful bumpy yellow blob we see. Its texture is like the fluffiest scrambled eggs, and I have read that it is cooked and eaten as such in Mexico—though I am not sufficiently adventurous to try it. If you see this in the morning, over the course of a single day it will turn tan and crusty, then brown and brittle. Break this, and you’ll get a cloud of black dust. The dust is spores, single cells that can spread on the wind and, in the right environment, repeat the cycle.

According to a recent hypothesis, the odd thing about Fuligo is that it not only eats protozoa as it oozes through the mulch, it actually incorporates some of their DNA into its own genome. This would be like me taking DNA from the asparagus that I ate last night and having the asparagus DNA woven into my own DNA—and that asparagus DNA would be found in the genomes of my descendants.

To briefly review, what makes Fuligo into Fuligo, and not asparagus or a human, is its genes. Fuligo DNA is transcribed to make RNA; that RNA either gets translated to make protein, or works as a catalytic RNA such as is found in the ribosomes. To a rough approximation, one gene encodes one protein or catalytic RNA. The sequence nucleotide bases in the DNA—A, T, G, and C—corresponds exactly to the sequence of nucleotide bases in the RNA transcript A, U (instead of T), G, and C. Likewise, the sequence of nucleotide bases in the RNA transcript corresponds in a precise way to the sequence of amino acids in the finished protein.

One hitch in this process is that the DNA often contains introns. Introns are sequences of DNA that occur in the middle of a gene, yet do not encode part of the finished catalytic RNA or protein. Eukaryotic organisms (like Fuligo, asparagus, and us) have lots of introns. As DNA is transcribed to make RNA, special enzymes snip the intron-encoded RNA out, and join together the remainder to make an RNA that can be much shorter than the DNA that it was transcribed from. The intron-encoded RNA is simply recycled.

Introns are a puzzle. They seem wasteful—the cell spends lots of energy replicating their DNA, making them into RNA, removing them from RNA transcripts, and recycling them. In fact, some people view them as “DNA parasites”: instead of an organism like a mosquito that reproduces at the expense of another organism, introns are DNA sequences that reproduce at the expense of another piece of DNA, the rest of the genome.

Most protozoa and a few fungi have particularly unusual introns. They are generally found in specific genes encoding the catalytic RNA of ribosomes. Class I introns are “self splicing”. They don’t need the help of any enzymes to do the cutting and pasting required to make a finished RNA. In fact, you can put RNA containing one of these introns by itself in a test-tube, and it will edit itself perfectly. The excised RNA will form itself into a stable little circle of RNA, and the rest of the RNA can go and do its job.

Different families of protozoa have different class I introns—the ones in different types of Tetrahymena look similar to each other, but different from the ones in different types of Acanthamoeba. Usually, the ribosomal RNA genes of these different protozoa contain one or two class I introns.

Fuligo is different. A group from Norway led by Steinar Johansen found that Fuligo’s ribosomal RNA genes have twelve class I introns. There’s a potentially easy explanation for this exuberance of introns. Duplication is a very common way for DNA sequences to evolve, so it’s possible that one class I intron could have been repeatedly duplicated. But the actual explanation is not so simple. Johansen found that most of the class I introns in Fuligo have no family resemblance to each other, so they’re not the result of duplications. In fact, one of the introns looks a lot like the ones from Tetrahymena. Another looks a lot like the ones from Naegleria. A third looks a lot like the ones from Acanthamoeba. These organisms, and a few others, are no more related to the Fuligo than you are—and yet, it looks like they contributed some DNA, specifically class I introns, to the dog-barf slime mold. A “family tree” of known class I introns shows this:

All the Fuligo introns are labeled Fse#### in bold; all the others are introns from other organisms. Generally, related organisms have related introns—for example, at the top of the figure, FseS1065 is a sibling of NmoL2563 and NmoL1949 and NaeL1926, which are all introns from related organisms in the genus Naegleria. Going down a little bit, you can see that the Fuligo introns FseS956, FseL1090, and FseL569 are closely related, and may have evolved by duplication from an ancestral intron. However, these are the only "sibling" introns in Fuligo.

Johansen proposes a wild hypothesis: The diverse protozoa eaten by the plasmodium stage of Fuligo have diverse class I introns. These are present (as the terrified protozoan is engulfed by the plasmodium) both in the protozoan genome, and as the little circles of RNA that are left over after the intron has been removed. It might be that the intron DNA gets mixed into the Fuligo DNA, or it might be that the intron RNA reverses its usual reaction—instead of snipping itself out, it pastes itself into a ribosomal RNA gene. Fuligo kills and eats the protozoan, but the protozoan reaches out of its grave and gives Fuligo a parting gift, a DNA parasite that it will never be rid of.

This is an unusual example of lateral gene transfer: the transfer of genetic material from one organism to another unrelated organism, uncoupled from reproduction. Typically, lateral gene transfer in Eukaryotes involves the transfer of a useful gene, one that enhances the fitness of the recipient, or something that is at least neutral. Here, we are shown the transfer not of a gene, but of a DNA parasite that may actually reduce the fitness of the recipient: a class I intron. Lateral gene transfer is rare in the Eukaryotic world (so I don’t worry about turning skinny and green when I eat asparagus), and this happened less than twelve times in the millions of years of Fuligo’s evolution. As Johansen says,

Perhaps the large number of introns accumulated in Fuligo [ribosomal RNA genes] reflects its natural behavior and promiscuous feeding habits and, thus, is a case in point of the phrase “you become what you eat.”

Eirik W. Lundblad, Christer Einvik, Sissel Rønning, Kari Haugli, and Steinar Johansen (2004). Twelve Group I Introns in the Same Pre-rRNA Transcript of the Myxomycete Fuligo septica: RNA Processing and Evolution. Molecular Biology and Evolution 21 (7), 1283-1293.

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