One Species' Genome Discovered Inside Another's

slyyy writes "The Universtiy of Rochester has discovered the complete genome of a bacterial parasite inside the genome of the host species. This opens the possibility of exchanging DNA between unrelated species and changing our understanding of the evolutionary process. From the article: 'Before this study, geneticists knew of examples where genes from a parasite had crossed into the host, but such an event was considered a rare anomaly except in very simple organisms. Bacterial DNA is very conspicuous in its structure, so if scientists sequencing a nematode genome, for example, come across bacterial DNA, they would likely discard it, reasonably assuming that it was merely contamination--perhaps a bit of bacteria in the gut of the animal, or on its skin. But those genes may not be contamination. They may very well be in the host's own genome. This is exactly what happened with the original sequencing of the genome of the anannassae fruitfly--the huge Wolbachia insert was discarded from the final assembly, despite the fact that it is part of the fly's genome.'"

mmm... home made mutants!

[cez]

This might have an interesting impact on the 10 year forecast to creating artificial life [slashdot.org] discussion from earlier today.

Re:scifi tag?

[TheMeuge]

The mitochondria have not been incorporated into the human genome. Mitochondria contains its own circular DNA structure, which exists and replicates independently of the genomic DNA. There must have been some gene loss/exchange, however, because many proteins necessary for mitochondrial structure and function are found solely in the genomic DNA.

mitochondria, chloroplasts, viral DNA

[brit74]

I haven't heard of a whole genome being inside another species. Although, the mitochondria (which are small energy producing factories inside most life - including mammals) have their own DNA which is separate from our nuclear DNA. Its DNA sequence resembles the sequence of single-celled organisms, which hints that there was a fusion of two different organisms hundreds of millions of years ago. Additionally, plants have chloroplasts (which do photosynthesis), and these are similar - they appear to have been cyanobacteria (independent organisms) that fused with another organism and became organelles within those cells. There are also bits of viral DNA in our own genome - it apparently fused into our DNA long ago. (In fact, you can trace evolutionary relationships by comparing the sequence and positions of these viral bits of DNA across species. Unsurprisingly, humans and apes share a remarkable number of matching viral DNA chunks.)

phoenix

[wizardforce]

roughly 8% of our own species' genome consists of bacterial and viral genetic material. some of the segments are nearly complete with at least one case of a virus being resurected called Phoenix. it seems to be a fairly common process, viruses can lose critical genes while trying to replicate in cells which can leave them unable to reproduce as usual, the genome becomes integrated into our own. there are also cases [herpes for example] which can integrate their genome with ours in certyain cells and effectively become dormant, they start the cycle again when and if certain conditions are met. http://www.nytimes.com/2006/11/07/science/07virus. html?ei=5088&en=492dd1d370217836&ex=1320555600&adx nnl=1&partner=rssnyt&emc=rss&adxnnlx=1163032655-5n RqAOkgWGeKvh/qQcSYCg [nytimes.com]

Re:scifi tag?

[wizardforce]

The mitochondria have not been incorporated into the human genome.

funny you mention that, apparently when two species merge into a symbiotic relationship like that not only is there genomic reduction but integration of parts of the endosymbiont's genetic material into the host genome. http://www.pubmedcentral.nih.gov/articlerender.fcg i?artid=166356 [nih.gov]

Re:scifi tag?

[izomiac]

You're right, but "some gene loss/exchange" would be an understatement. IIRC, there are about 1600 mitochondrial genes, and only about 20 of them are actually on mtDNA (most of those are tRNA). So the rest have been integrated into the "host" genome. This is actually an ongoing process and gene transfer happens a lot more frequently than you'd think. Mitochondrial genes that get inserted are called NUMTs and have actually been associated with human disease.

Re:scifi tag?

[RDW]

'There must have been some gene loss/exchange, however, because many proteins necessary for mitochondrial structure and function are found solely in the genomic DNA.'

In fact _most_ of the genes that encode mitochondrial proteins are now in the nucleus, presumably a result of ancient DNA transfer from the primordial mitochondrial genome to the nuclear genome, so the parent post is substantially correct. The modern mitochondrial genome is pretty vestigial (smaller than that of many viruses). The original article speculates that a Wolbachia bug might one day evolve into an organelle by similar processes, and suggests that the existing insert may have a selective advantage for the host.

Re:scifi tag?

[catbutt]

So the genome of the e. coli in our intestines is part of our genome? I don't think so. Mitochondrial dna, yes, because mitochondria are not considered separate organisms, but e. coli are. Admittedly, the lines can be a bit blurry, but still. One big difference is that mitochondrial dna normally passes from parent (specifically mother) to child and ancestry can be traced with it, but e. coli can move "horizontally" much more readily.

Re:scifi tag?

[eli pabst]

There are mitochondria in both sperm and egg. Offspring generally inherit only the mothers mitochondria, though their have been a few reported cases paternal mitochondria inheritance. I believe the theory is that while they are present in both male and female gametes, the males mitochondria are degraded almost immediately after fertilization.

Evolutionary Tree not a Tree

[Tablizer]

This may mean that the idea of the "inheritance tree" needs to be revisited. One speculation for the Cambrian Explosion is that a genetic system evolved that made inter-species gene swapping easier (assisted by microbes and viruses). This could speed up evolution by swapping "good ideas". Species A could steal the eye design of species B, and species B could steal the immune system of species A, etc. But it may make paleontology and fossil evolution interpretation tricky. (As species grew more complicated over time, swapping became more difficult.) Instead of an evo tree in the textbooks, we may start seeing Directed Acyclic Graphs.

Re:mitochondria, chloroplasts, viral DNA

[TheRealMindChild]

Apes... don't have... tails.

Re:Mebbe it's just me but

[glwtta]

I think it would be interesting to take a person's stem cell and try to remove all the "junk DNA" from the nucleus

Uh huh, and how exactly do you propose to do that? (also, doing this on a human seems like a pretty bold move)

People tend to throw around "junk DNA" without really specifying what they mean. For humans, we know that about 1.5% is coding, about 4% is highly conserved (so, probably very important) and we suspect that a fair amount more is involved in transcription regulation (there's been a lot of activity in that particular area recently), but we have a very faint idea of how much that would be. I saw a talk a few weeks ago where they claimed that nearly all non-coding DNA is involved in this function; that's not a widely held view, though.

It seems likely that since there are so few actual genes and they are so sensitive to mutation, then a highly redundant and more "flexible" mechanism for transcription regulation is one of the primary mechanisms for evolution.

So yeah, I am not sure where the popular perception that non-coding DNA is considered to do nothing comes from.

Oh, and as someone already pointed out, the number of chromosomes a particular organism has is completely meaningless (chickens have 78, some primitive plants have hundreds or even thousands).

Actually, it's very easy to imagine

[Moraelin]

Hard to imagine that viral DNA is 5% of our genome without having any impact..

Actually, it's very easy to imagine. Transcribing DNA to proteins happens between a START and a STOP marker. If those markers are lost -- heck, even if just the START marker is lost -- then that piece of code is never "executed". In programming terms, it's commented out.

And, yeah, your genetic code contains a whole bunch of commented-out sequences. Dunno, I don't have much trouble believing that they have no impact whatsoever :)

Re:scifi tag?

[Spurion]

I'm wondering how they get there in the first place

The same way they get into any other cell. Eggs, like all cells, are produced by cell division. It's not exactly the same process (meiosis rather than mitosis) but many aspects are the same.

Re:scifi tag?

[eli pabst]

There is some info on it at the Wikipedia page for mitochondrion:
http://en.wikipedia.org/wiki/Mitochondrion#Replica tion_and_gene_inheritance [wikipedia.org]
http://en.wikipedia.org/wiki/Mitochondrial_DNA#Mit ochondrial_inheritance [wikipedia.org]

I don't know what kind of access you have to scientific journals but this abstract has a pretty good description of sperm mitochondria and how they are degraded via ubiquitinylation (a common degradation pathway)

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed &Cmd=ShowDetailView&TermToSearch=12672125 [nih.gov]

Hope that helps.