Another Explanation for Multicellular Life

DrJay writes "Hot on the heels of Slashdot's coverage of a controversial model for a viral origin of the multi-cellular branch of life, Nature has published an alternative model that has nothing to do with viruses. Ars Technica's science journal has the rundown on the differences between these proposals." From the Ars article: "It's funny that this proposal for the origin of Eukaryotes should hit the popular press at a time where Nature has just published a hypothesis regarding the formation of the nucleus that has nothing to do with viruses, but everything to do with parasites. The parasites in this case are molecular: Type-II introns. These DNA sequences exist in both eukaryotes and bacteria, where they can insert in the middle of genes without causing harm because they can undergo chemical reactions by which they remove themselves from the RNA messages the genes make."

Re:History, not science

[hunterx11]

While we may never know, I do think this is a different situation. We can't really recreate the conditions under which language initially developed, but no doubt we will eventually be able to synthesize multicellular life.

Re:All we know is that we don't know.

[LordofEntropy]

Some terms and stuff for the laymen:

Eukaryotes are 1 of 3 domains of life in the current popular classification of life. The other 2 domains are Prokaryotes(single cell organisms) and Archaea(these tend to be the thermal vent/volcanic organisms, extremophiles.)

Eukaryotes are characterized by being mostly multicellular organisms(that is made up of more than 1 cell), and those cells have membrane bound organelles(think of little organs but for cells). Eukaryotic cells also have a nucleus which protects and regulates access to the DNA material. In the other domains the DNA is just floating around.

When the cell goes to make proteins, the blueprints are found in the DNA. When a template for a protein needs to be made, it is copied from the DNA, processed and then transported out of the nucleus to be further process into a protein, this template is called mRNA(messenger RNA).

In Eukaryotes you also find what is referred to as "junk DNA". Although this term isn't entirely accurate, this junk DNA is called such because no active proteins are made from the DNA sequences in this region. These non-coding regions are cut out from the template mRNA are called introns. The segements that are kept are called exons.

Basic rundown of some of the concepts the article refers to.

Re:Laymans terms

[theredmenace]

Depending on how much you know, skip ahead: There are two kinds of cells. Prokaryotes (bacteria) and Eukaryotes ("higher" organisms... plants, animals, fungi, etc). Viruses are officially not considered to be alive, because as part of the cell theory, cells must be capable of replication, which they are not, they need other cells (hosts), just like prions (proteins that act in a viruslike fashion). The debate about the "life" of viruses rages on. This giant uber virus shows a lot of sofistication, perhaps suggesting that viruses had some other role to play. The original article suggests that viruses like the giant one in question could be the reason for the nucleus. The current belief is that certain organelles, specialized structures in the eukaryotic cell, arose from a more primitive cell injesting another cell, but instead of digesting it, forming a relationship with it. This is where chloroplasts and mitochondria come from (both of which are used to "power" cells). The first article suggests that the nucleus arose in a similar way, only what was enveloped was a virus. Additionally, that article says viruses have evolved the opposite way the rest of live has, by shedding excess DNA instead of adding to it. This other article says that the nucleus developed as a way to protect the DNA from "introns" that floated off of these newly aquired mitochrondria. Most of DNA, especially higher DNA, codes nothing. It is just there to "pad" the good stuff. When a protein is going to be coded for, the DNA unwinds, and the section is copied. The copy is made of RNA, a single strand (not a double helix), which is then translated into the protein. Before the translation though, the extra stuff has to be cut out, and it is. The extra stuff has markers to tell the cell where to cut it and where to stop and how to patch it all together. The stuff that is cut out is called INTRONS. The good stuff is called exons. The exons tell the protein what to be. Think of it as trimming the fat. Just like you can tell the difference between the good and the bad, and trim accordingly, so can the cell. From what I understand, the introns from the mitochondria had the ability to insert themselves in the DNA. This causes what is known as a phase shift. Basically, you have all these lines of code, and inserting a bunch of extra code somewhere in the middle screws up the ability to either find the gene, or if it actually gets translated anyway, the protein is non functional. The nucleus is a defence, it keeps the introns out by barriering itself in. Transcription of DNA (copying to RNA) occurs in the nucleus, and translation (RNA -> protein) occurs in the cytoplasm outside the nucleus. The two conflict with one another, but could in theory be integrated, but it's not too likely. I personally doubt the nucleus is a virus, the nuclear membrane isn't really the right material. The question is whether these scientists have actually FOUND these introns floating around attacking DNA or not. I can't access the full article.

Re:Laymans terms

[frenchs]

Keep in mind that in biology always has exceptions, so while the following will give you a basic background, it's NOT a textbook. See the links for some reasonable pictures to describe what I'm talkin' bout.

Central Dogma

• DNA is used to create RNA, which is used to create a amino acid chain, which folds into a Protein.
  
  
• Protiens are different from each other by their structure, which is detirmined by the sequence of amino acids which were assembled from the RNA sequence.
  
  
• RNA sequences are different based on the DNA sequence that was used to make them, and therefore encode different protiens based on the DNA sequence that we used to make them.
  
  
• (this is the important one) Structure = Function. The way that a protein is shaped directly influences what it does.
  

So if you follow back up the chain, DNA is responsible for creating protiens which perform biological and chemical functions. DNA->RNA->AminoAcidChain->Protein

http://www.accessexcellence.org/RC/VL/GG/central.h tml [accessexcellence.org]

Prokaryote/Eukaryote

Life is classified into two major groups, prokaryotes and eukaryotes. They fall into these two groups based on what kind of cells they have inside them.

Prokaryotic cells are simple, not a lot of really complex organization inside of them. Bacteria like E.coli fall into this group. Prokaryotes can do some cool things with the incorpration of foreign DNA (other cells, viruses, etc.) into their own DNA.

Eukaryotic cells are more complex, they have more "organized" inside them. The biologists call it "membrane bound organelles". Humans have eukaryotic cells.

http://en.wikipedia.org/wiki/Prokaryote [wikipedia.org]
http://en.wikipedia.org/wiki/Eukaryote [wikipedia.org]

Introns/Exons

Introns are what you hear referred to as "Junk DNA". However it's becoming apparent that this is the worst naming possible, as there are theories about it's presence being an activator for other processes which take place during DNA replication.

Exons are the sections of the DNA that are directly tranlated into the coresponding mRNA

Here is a DNA strand, the "E" are exons, and the "o" are introns.
EEEEEEEEEEEEooooooooooooooEEEEEEEEEEEEEEEEoooooooo ooooEEEEEEEEEE

Now here is the coresponding RNA, the ^ denotes a splice point where introns were removed. (This is what's used to create a given protein)
EEEEEEEEEEEE^EEEEEEEEEEEEEEEE^EEEEEEEEEE

http://en.wikipedia.org/wiki/Intron [wikipedia.org]
http://en.wikipedia.org/wiki/Exon [wikipedia.org]

Summary

So basically this article is saying that there are parasitic sequences of non-coding DNA which survive simply because they are in the DNA of a sequence which survived replication. But in eukaryotes, these "non coding" secions starting causing havoc in the cell and cause altered function.

Here is a analogy, albeit a tasteless one:

Imagine a room full of mimes (yes, mimes). Normally, they would sit there, pretending to be a box and not saying a word. Now imagine there is one mime that snuck a baseball bat into the room and started clubbing all of the other mimes in the knees. What do you think is gonna happen? Yep, they are no longer mimes.. they are now just angry dudes with white face paint on screaming at the top of their lungs.

Cells with DNA in them = Room of mimes
Parasite = baseball bat equiped mime
Havoc = clubbing knees
Altered Function = screaming instead of being mime-like

http://en.wikipedia.org/wiki/Mime_artist [wikipedia.org]

Biologists, feel free to correct any gross errors here. However, I stand by my analogy.

-s

Re:I'm a noob. How do I read this article?

[cheesygrapes]

There's a link to the abstract from slashdot and the abstract has a link that sayeth: "full text"

Re:I'm a noob. How do I read this article?

[AndyKron]

Thanks cheesygrapes, but I think I'm missing something. Do you mean the link at the top that takes me to Nature? I clicked on "full text" at Nature, but then I was sent to a page that said I needed a subscription.

Re:huh?

[AJWM]

Offhand I can't think of a multicellular organism that doesn't comprise eukaryotic cells.

Sure, there are things that are colonies of prokaryotic cells, but those are recognized as organisms at the individual cell level, not the colony level. Do you have a counterexample?

Of course, there are plenty of single-celled eukaryotic organisms, and I think that's what the article is really talking about.

Re:Laymans terms

[Henge]

Actually, it's a misrepresentation to assume introns are 'parasitic.' There's a good amount of speculation these days that introns actually confer an enormous selective advantage on their bearers, because they could facilitate 'swapping' of exons between genes during replication in a way that permits new genes to arise. Imagine this scenario: Consider two hypothetical genes with exons "A,B" and "C,D" interspersed by introns "o" with some degree of sequence similarity. AAAAAAAAoooooooooBBBBBB and CCCCCCCCoooooooooDDDDDD during cell division, the genes are duplicated and some "crossing over" (that is, homologous recombination) occurs between strands in a way that is facilitated by similar sequence. As a result, one copy each of genes "A,B" and "C,D" swap exons and become "A,D" and "C,B" AAAAAAAAoooooooooBBBBBB X crossing over of homologous strands CCCCCCCCoooooooooDDDDDD Voila! You now have two new genes. Considering the fact that exons are often generalized as acting as discrete, independent units once they are translated into two proteins, you've created two new proteins with a potentially meaningful switcheroo in function. In this way, new proteins can evolve by swapping independent modules. So don't knock the introns.

So much misinformation

[bllius69]

For some basic (and free info), try NCBI's bookshelf: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=B ooks [nih.gov] Molecular Biology of the Cell is nice, as is Biochemistry, or The Cell. (Note: Koonin works at NCBI).

Or search Wikipedia, google, etc.

1. "Most of the DNA in the cell is wrapped in a fat and protein membrane."

Most of the DNA in "all" three kingdoms are wrapped up in proteins. In eukaryotes there is a membrane that surrounds the entire set of chromosomes (except during cell division) called the nuclear membrane. Chloroplasts and mitochondria are also surrounded by membranes. All membranes have proteins in them. In Prokaryotes, the entire cell is surrounded by at least one membrane, and the DNA is inside of this in the cytoplasm. It does not float freely. In prokaryotes, most chromosomes are circular (but not always) and most organisms have one chromosomes (but not always). In eukaryotes, most organisms have multiple linear chromosomes.

NB: Membranes are comprised of lipids and proteins and in some cases other molecules like cholesterol. Lipids are also known as "fat" and there are many different types.

2. Central dogma/transcription/translation.

In prokaryotes, transcription (copying DNA to mRNA) and translation (translating the RNA to create polypeptide (protein) chains, done by the ribosome) are coupled. In eukaryotes it is uncoupled as the RNA has to be transported out of the nucleus through the nuclear pore, where the mRNA is then translated by ribosomes in the cytoplasm, or by ribosomes attached to the ER and exported.

3. Prokaryote/Eukaryote introns

Introns are not eukaryotic-specific. All three branches of life have introns, however, they are far rarer in the archaea and bacteria (especially rare). Some introns can self-splice (remove themselves), while others do not. Lots of different "types" of DNA can move themselves around, insertion sequences, transposons, phages, viruses, conjugative DNA, etc. This movement of DNA is a driving force in evolution itself, not merely in a host organism protecting itself from invasive DNA, but in the evolution of novel protein functions.

4. Single/multicellular

There are single-celled eukaryotes (yeast cells) and there are prokaryotes that form developmentally specialized conglomerations of cells (biofilms, cyanobacterial chains, mycelial hyphae) where some cells are specialized as compared to others. Many prokaryotes can signal to, as well as receive signals from, other cells.

5. Mimivrius

Mimivirus is interesting, but it is an extreme outlier. More work on the full range of virus forms and genome ranges will help in this arena. Some of the metagenomic projects will definitely help in this area. It's like attempting to hypothesize the evolution of mulicellular organisms based on the blue whale.

6. Introns and domains.

Proteins fold into 3D structures to perform functions. The basic unit is a domain, which are units that can fold into a 3D structure themselves and perform some function (basically). Exons and domains are not a 1 to 1 relationship. IMO, intron evolution has a lot more to do with alternative splicing events and regulation in developmental pathways than it does in driving new functions for genes (you can duplicate genes and domains without introns/exons).

7. Membrane evolution.

Membrane compartmentalization is a key step in evolution. Interestingly the prokaryotes (archaea and bacteria) have two different types of lipids, suggesting that in the early stages of this evolutionary step that two pathways were chosen, and both have been maintained since that time. Again, another point in evolution is not that one system is always better than another, but that endpoints are achieved through multiple pathways.

8. Koonin et al., hypothesis.

Their hypothesis is interesting. I haven't read the paper, but I have seen Koonin's seminar from a few months ago. Unfortunately there is so much we don't know yet. His ideas may be skewed towards analyses based simply on comparative genomics and not enough on biochemistry.

introns & junk DNA

[supertsaar]

Introns and Exons are found within a gene. They are important for such things as alternative splicing, which can be used to generate diversity 'on demand', for instance this plays a part in the immune response.
It seems that Introns are considered part of 'junk DNA', but given the fact that in some cases introns play an important part I think this is unfair to introns....

Re:introns & junk DNA

[espressojim]

Introns haven't been considered junk in quite a while. It's been know that there are some regulatory regions hiding out in introns.

For more interesting 'proof', see my paper in febuary nature genetics about conserved noncoding regions under selection - one of the strongest signals for selection was seen in intronic regions. We found parts of introns that were under as strong selection as coding regions.

It's nowhere NEAR junk DNA.