Ancient DNA Redux: 700-Year-Old Virus Resurrected from Frozen Caribou Dung

Under nine feet of ice, frozen for 700 years, from DNA extracted from bits of caribou dung, a viral genome has been recovered and brought back to life.   Don’t worry this isn’t a case of mad scientists resurrecting the black plague for nefarious purposes.  This is the story of some inquisitive scientists investigating past environments by looking at frozen caribou dung pulled out of an ice core in the Northwest Territories of Canada.  Apparently caribou seek out permanent ice patches in the warm summer months to escape mosquitoes and to cool down.  While there they do what caribou do and some of those remains become part of the growing ice field.   The partially digested plants that passed through that caribou stomach have been frozen for 700 years.   Now they are a tiny little time capsule holding clues about the climate and vegetation of a remote area in northern Canada.

In a study just published scientists looked specifically for viral DNA in these frozen remains.  By sequencing all of the DNAs extracted from the feces they found one entire viral genome and another partial one.  Both of these viruses are similar to viral genomes than infect plants today.

To assess if the genome sequence they obtained was really a complete genome sequence of a virus with no mistakes due to the age of the sample, the scientists took the sequence they generated and injected it into some plants.  Soon they found that some of the plants began to generate more viruses of the same type, evidence that the virus had been taken up by plant cells and caused them to make more viruses.  Had there been many mutations in the DNA due to degradation those mutations would have been expected to disrupt the normal functioning of the virus rendering it incapable of infection.  But it was able to make a fully function virus capable of infecting modern plants.

In effect they resurrected a virus that had been in cold storage for 700 years.   This isn’t as impressive as the huge virus revived from a 30,000 year old ice core which I wrote about earlier this year (Ancient DNA Comes to Life: Giant Virus Resurrected from Siberian Permafrost) but it is still quite impressive.

A critical and as yet unanswered question about ancient DNA is:  how long can DNA survive?

Many scientists previously believed, though without much data, that long strands of intact DNA could survive no more than a few hundred years even if some DNA fragments might be able to survive for millions of years.  The resurrection of a 30,000 year old virus told us that DNA can survive under good conditions with very little damage for thousands of years.

This new viral genome provides another window into the stability of DNA overtime.  Prior to trying to sequence viral genomic material from caribou dung the investigators had tried to copy large fragments of mitochondrial DNA and presumably other plant and animal DNA in the dung and found that they were broken in many fragments.  Yet, they were able to recover the entire viral genome as one piece.   They proposed that the amazing fidelity of the sequence after 700 years is due to the genome being protected in a viral capsule.  That housing seems to have protected its genome to a much greater degree than the plant and animal DNAs in the same sample.

One strand of a DNA molecule showing all the places where DNA will be chemically modified over time.  Individual pieces of DNA molecules can theoritically survive hundreds of millions of years but it will be broken into many small pieces and the molecules rearranged making it impossible to determine the code of DNA.   Sequencing of the code becomes more and more difficult the more the molecule is modified so even if there are 30bp fragments left it might be impossible to read that code.  In the case of the 400,000 old human bone sequenced its DNA was extremely damaged and many fancy new methods of "repairing" the dna had to be employed before they could read a small portion of the code.

One strand of a DNA molecule showing all the places where DNA will be chemically modified over time. Individual parts of DNA molecules can theoretically survive hundreds of millions of years but because the DNA molecule will have broken into many small pieces and the molecules rearranged it will be impossible to determine the code of DNA. Sequencing of the code becomes more and more difficult the more the molecule is modified so even if there are short 10bp fragments left it might be impossible to read that code. In the case of the 400,000 old human bone from Sima De Los Huesos sequenced its DNA was extremely damaged and many fancy new methods of “repairing” the DNA had to be employed before a small portion of the code could be sequenced.  Here DNAs were preserved in ice and the additional protection of a stable protein coat may have protected the viral genomes even more.

The lesson here is that we still don’t fully understand the conditions under which DNA is able to be preserved and how long that DNA can be preserved.  Simple chemical studies suggest that DNA will be damaged relatively quickly and yet we now know that DNA has survived much longer than those simple chemical assumptions would indicate is possible. This tells us that there are other mitigating factors.  The DNAs could be protected by having many proteins bound to them. Maybe quick drying of a sample removing the DNA from the presence of water will reduce the hydrolytic effects of water.   In the case of the caribou DNA, this DNA has been essentially frozen for 700 years and we know that cold slows the process of DNA decay.  In this case the viral capsule particles may have provided added protection.

At the same time the technology developed to recover DNA from ancient samples has advanced dramatically in just the last five years.  Methods of extracting DNA that don’t damage the molecules further have been developed.  The most exciting development has been that of treatments that have allowed damaged DNAs to be repaired prior to their sequences being obtained.  All of these things have allowed us to more reliably obtain genomic information from organisms that have long since expired.  This genomic information is allowing up to piece together the history of many animals and is even changing much of what we know about our own genetic history.  Soon thousands of people who have died over the past several thousand of years will be sequenced allowing for far better ancestry analysis than is available to us today which is based only on the genomes of those that are living.

Comments

  1. Reblogged this on gottadobetterthanthis and commented:

    A little about what we know and what we don’t know.

    Like

Comments or Questions?

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: