Conditions in Antarctica's McMurdo Dry Valleys are so hostile they've been compared with those found on Mars. Photo / File
Conditions in Antarctica's McMurdo Dry Valleys are so hostile they've been compared with those found on Mars. Photo / File
Herald science reporter Jamie Morton is profiling a series of new studies taking place in Antarctica, before his return to the frozen continent next month. Today, he talks to the University of Waikato's Dr Adele Williamson.
Antarctica's McMurdo Dry Valleys are so unwelcoming of life they've often been likened to conditions we might find on Mars.
It's even possible this extraordinarily brutal environment might eventually guide our search for life beyond Earth.
What scant moisture there is in this landscape – which, contrary to how we picture the frozen continent, is actually ice-free - gets blasted from the ground by some of the fiercest winds on the planet.
Temperatures plunge as low as minus 60C in the winter.
Only when they edge above 0C in summer, for as little as 25 days, is liquid water available through the melting of sub-surface ice.
Seasonal swings cause their own problems. In only a day, the mercury can shift by up to 20C, between multiple, dramatic cycles of freezing and thawing.
On top of that, the summer light brings damaging levels of UVA and UVB.
It defies all logic that any organisms survive here.
But they do.
More remarkably, scientists have discovered a fascinating amount of diversity among the microbes that cling to life within the soils of this extreme polar desert.
But, even for these hardy bacteria, living in the Dry Valleys comes at a cost.
The unforgiving conditions are highly damaging to DNA, which stores the hereditary information needed to build and maintain any organism.
This means that, to exist, these microbes have to boast incredibly efficient repair systems.
Even so, conditions in the valley systems are so toxic to genetic material they can break strands of DNA completely – and the little nutrients they can draw from the soil give them few options to repair the damage.
"I want to know if Dry Valley microbes have different DNA repair pathways compared to model organisms - and a sneak peek at the sequencing data we analysed have so far indicates that yes, in some cases, they do," she said.
"Do these repair pathways use completely different enzymes? Are the enzymes faster and do they have unique ways of recognising or repairing damages? Do they work better at low temperatures?
"DNA repair generally involves co-operation of several enzymes in different steps: how do the individual components interact? How do they coordinate their activities?"
A study to take place in the McMurdo Dry Valleys seeks to understand how hardy bacteria living there repair their own DNA. Photo / File
This question is especially important, because most of what we understand about bacterial DNA repair - and in fact about most cellular processes - comes from a few well-studied organisms that are easy to grow in a lab.
But it is estimated fewer than 1 per cent of bacteria can be cultured this way.
"What we know so far about the microbiota inhabiting in the Dry Valleys is they have very little similarity at the DNA level to these model organisms and very few can be grown in the laboratory," she said.
"So, this is an opportunity to take a direct look at a part of life on our planet that we have never seen before."
And perhaps that life can tell us about other planets.
"As well as increasing our understanding of the organisms inhibiting the harsh yet fragile Antarctic ecosystem, the Dry Valleys are considered a good model of the Martian climate," she said.
"Studying the molecular mechanisms that enable its inhabitants to survive can provide clues to how extraterrestrial life could look."
As you'd expect, the Dry Valleys' microbiota has adapted specifically to this harsh climate, which itself is being slowly changed by our own activities.
The ozone hole, which peaked over Antarctica in 2006, is reducing in size thanks to a ban on CFCs, yet is still responsible for an increased UVB incidence in recent decades.
It is also impossible to imagine that human-driven climate change won't come with consequences for the region.
Where life isn't cushy
Since many of the Dry Valley microbes won't grow under lab conditions Williamson describes as comparatively "cushy", she's drawing on a metagenomics approach to discover their DNA repair genes.
Despite their near-alien conditions, the soils of Antarctica's Dry Valleys are home to an abundance of life. Photo / File
"Briefly, for a particular sample site, the aggregate DNA of all organisms within the soil sample will be sequenced, and I will use computer algorithms to predict which DNA sequences encode proteins involved in repair processes."
Professor Craig Cary and others at the Waikato-based International Centre for Terrestrial Antarctic Research have already archived more than 2000 soil DNA samples.
These have been gathered from sites as far flung as the Central Transantarctic Mountains and Cape Adare in Northern Victoria Land, with field support from Antarctica New Zealand. The team plans to collect more in the next field season.
All the bacteria have been sequenced for 16S rRNA, which gives a measure of how closely related the bacteria from the site are to other known bacteria.
The metagenomes of more than 100 sites have also been completely sequenced and assembled into large enough segments to predict pathways, thanks to an award from the Joint Genome Institute's Microbiome Project and the Community Sequencing Programme.
"My first task will be to annotate these metagenomes, which means figuring out which parts encode proteins, and what these proteins do," Williamson said.
The University of Waikato's Dr Adele Williamson. Photo / Supplied
"To make an analogy, the DNA sequences are like strings of letters and annotation involves finding the individual words then ascribing them a meaning."
This generally involves comparing the sequence of the gene - or rather the protein it encodes – to other proteins with known function.
This becomes more difficult the more divergent the protein is from known homologues.
"To return to the analogy, if two words are very similar you can probably deduce that 'katt' means 'cat' with reasonable certainty, but with more distant relationships you may only be able to predict that the word is a noun, or at a minimum, only that it is 'a word'."
Once she has figured out which enzymes are those being used for DNA repair, she will produce them in an expression host.
This process will involve putting the gene encoding the enzyme into a bacterium that can then be grown easily in the lab, and next, tricking it into making an enormous quantity of the protein.
Thousands of samples have already been gathered by the University of Waikato's Professor Craig Cary and others. Photo / Christine Cornege
"Then I will break open the cells and remove the contaminating host proteins leaving only the enzyme that I am interested in and can now study in pure form."
She will test the activities of these proteins using small synthetic pieces of DNA with well-defined damages chemically incorporated into them.
"I will also test how the proteins interact: does one require another protein to bind the DNA? Does it enhance the activity of another?"
With colleague Professor Vic Arcus, she will attempt to determine the 3D structure of the repair enzymes bound to DNA damages using what's called X-Ray crystallography.
That means growing crystals of the protein bound to the DNA substrate - and then shining X-rays on them to determine the molecular structure.
"This will enable us to see, for example, details of how the enzyme binds to the DNA and where the chemical reaction that is taking place during the repair process occurs."
Once she has a reasonable idea of how these repair proteins functioned, she will transplant a group of genes from one of the repair pathways them into E. coli to test whether this imparts DNA-damage resistance – or whether she can effectively change this mesophilic laboratory "pet" into an extremophile.
Her ultimate hope is simply to glean more insights into how these hardy bugs survive where most life can't.
"In particular, I want to understand how specific differences between the protein complements of these bacteria and model organisms endow them with such resilience.
"Are their DNA repair systems merely tweaked by small changes? Or do they, as we suspect, possess some completely new methods of maintaining genomic integrity?
"We would also like to understand novel DNA repair processes from the enzyme's point of view: are there different routes to repairing the same damages from what we already know?
Conditions that microbes are adapted to in Antarctica's McMurdo Dry Valleys can't be replicated in the lab. Photo / Supplied
"Are there different enzyme structures that can be used to do this? We also hope that some of the new enzymes that we expect to find can be employed in biotechnological applications, or used to develop new tools in the future."
Cold-active DNA modifying enzymes are particularly sought after because they can preserve samples without their DNA or RNA becoming degraded.
"If we detect novel modes of action in some of these enzymes this could provide the basis for developing completely new technologies, she said.
Temperatures range from minus 60C in winter to over 0C in summer and seasonal shifts also bring multiple cycles of freezing and thawing in single days. Photo / File
"Consider, for example the CRISPR-Cas revolution: basic research was the primary motivation that lead eventually lead to development of this ground-breaking tool.
"Not that I am expecting we'll discover the next CRISPR-Cas: just making the point that keeping an eye open for practical applications while doing fundamental research is a pretty good way to spend your time."
Williamson's study is supported by a $300,000 grant from the Marsden Fund.
