DNA – it’s not just information, duh

In 1953, James Crick and Francis Watson discovered the source of information in our cells – DNA. This spiral of bases attached to a sugar-phosphate backbone is the ultimate information storage: it is stable, trustworthy, easy to repair and is divided up so that a cell’s offspring contains the same information as the original cell. But it’s not just information storage that DNA is apparently good for: researchers report in PLOS ONE that some bacteria like to eat it too.

The greedy DNA eater is Haloferax volcanii, an archeabacteria. Haloferax volcanii (Hfx. volcanii for short) is not just interesting because it can live in very salty conditions; it also has several copies of each chromosome, composed of DNA and backbone proteins. That is not unique – we humans are diploid, as we have two copies of each chromosome. Hfx. volcanii can have more than twenty copies of each chromosome. Now, why is that a good idea? One theory is that the additional copies are redundant copies for safety, similar to making copies of your files on several external hard drives. But for repairing damaged DNA, cells need to have already quite evolved DNA repair mechanisms, the researchers argue. Looking for an alternative hypothesis, they investigate whether DNA is used not just for what it represents – information, but also for what it is made of – bases, sugar and phosphate.

They grew bacteria in a broth with all nutrients they need for growing, except for phosphate. Within 140 hours, the bacteria had grown, and the number of bacteria in the broth doubled three times. The researchers then measured the number of chromosomes per bacteria in the stationary phase, when the bacteria have stopped doubling quickly. Bacteria that grew with plenty of phosphate in the broth had 24 copies of each chromosome, but bacteria without any phosphate only had 2 copies of each. Phosphate in the DNA could be used to fuel the growth without external phosphate, especially as other sources of phosphate in the cell, like ribosomal RNA, is not reduced in these bacteria.

When the researchers then added phosphate to the flask of bacteria that previously were without phosphate, the bacteria managed to accumulate 40 chromosome copies per cell within just 23 hours. So when the bacteria have an external source of phosphate, they take it up quickly and replenish their phosphate storage as DNA, accruing chromosome copies.

DNA as food? It does sound a bit outlandish, the quintessential code for “information” reduced to mere nosh. But the researchers suggest this as a hypothesis for the origin of DNA. Most theories on the origin of life suggest that RNA, a similar molecule to DNA but made of just one strand, was the first molecule to store information in organisms. DNA is more stable than RNA, and eventually replaced it as information storage. The authors suggest that the first cell with several chromosome copies actually did not use DNA as genetic storage. Rather, it was used for food first, and for information storage later, because of its stability. This is an intriguing hypothesis, offering an alternative view to the “RNA world”. As the researchers themselves admit, this view “might not be true and cannot be proven”. But different it certainly is.

Original research paper on PLOS ONE: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0094819

Shaken, not stirred

Olives are part of any good Greek salad – or Bulgarian shopska salad, or any other variation of the tomato-cucumber-olive salad that heralds summer. From fat, plump Kalamata, to the sort of sad, de-stoned kinds straggling at the back of your fridge, all types wriggle their way in.

Somewhat surprisingly, as researchers noted this week in PLOS One, a huge diversity exists not only on supermarket shelves, but also in Iranian olives. What’s more, this variation is separate from the large variation in olives that grow in the Mediterranean. To find out whether olive types in the two areas are related, the researchers looked at SSR markers, regions in the olive’s DNA in which short combinations of bases encoding information are repeated many times. Looking at the length of SSR markers in different varieties, the researchers work out which olive types are related and which aren’t. They find that olives in the Mediterranean and Iran probably separated early on in the olive’s history. Olives are cultivated only in a few regions of Iran, but the research shows that Iranian olive types vary greatly. Most of the diversityin Iran’s olive trees is actually found in patches of trees and small groves, abandoned from cultivation or remnants of a former cultivation as “holy trees”.

Olive trees in Cyprus.  (By Anna Anichkova (Own work) [CC-BY-SA-3.0 ], via Wikimedia Commons)
Olive trees in Cyprus.
(By Anna Anichkova (Own work) [CC-BY-SA-3.0 ], via Wikimedia Commons)
Why should we care? Iranian olive trees are not fickle: some survive at low temperatures nearly unheard of in the Mediterranean, others withstand over 40°C, while some grow at high altitudes and poor soil condition. In face of dwindling diversity, an unexpected source of genetic variation is rare and welcome news. A large pool of diversity seems like a good hedge of bets for an uncertain climatic future, but low numbers and threats to their environment endanger also this olive source. Thankfully, some Iranian olive trees bear large fruits, which bodes well for the summer salads of our future. For which a good recipe, as always, comes from smitten kitchen: smittenkitchen.com/blog/2013/05/greek-salad-with-lemon-and-oregano/

Original paper in PLOS One: www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0093146