Tuesday, 30 July 2013

Breaking The Fourth Wall?

In 1962, the American microbiologist Carl Woese completely redefined the way we categorize life at its highest level. For years, scientists had recognised that life could be split into two groups: the prokaryotes and the eukaryotes. The eukaryotes were made up of plants, animals, fungi and protoctists while the prokaryotes comprised just one group, the bacteria. This classification scheme was based purely upon physical observations of cells in both groups.

Carl Woese found something rather different. Instead of looking down a microscope, he observed the genetic codes of these groups. He found that there were not two, but three different groups of life. The bacteria were one, the eukaryotes another; the third were the archaea. Previously, theses strange prokaryotes were lumped in as a group of bacteria. Based on their genetics, however, the archaea actually constitute a completely separate branch on the tree of life. While his scheme received criticism from his peers, Woese's 'three domain system' is the accepted way of classifying life.

Now, discoveries from Chile and Australia might potentially change this well established view of our planet's organisms. Viruses are one of the most contentious subjects in biology. Whether they are alive or not is a debate which has raged ever since their discovery. The general consensus is that they are not. However, recent discoveries blur the boundary between living and non living, cell and virus.

The Pandoravirus, so large it can be seen with a regular microscope.
The Mimivirus was the first blip on the radar. Discovered in 1992, it was actually mistaken for a bacterium due to its size. It was only in 2003 that it was identified as a truly massive virus. What makes it interesting is that, unlike almost all other viruses which require a host to manufacture proteins, it possesses genes which can create substances independent of a host. Virtually all viruses are dependent on a host in order to 'live.'

The Mimivirus was the first in a line of viruses which could partially function without a host, making it something of a hybrid between the host-dependent world of viruses and the free-living world of cells. Megavirus chilensis was the next discovery. Slightly bigger than the Mimivirus at 420 nanometres in diameter, it helped demonstrate that giant viruses were not absolute anomalies and actually constituted a separate group of viruses. The discoveries from Chile and Australia have not only added to the giant virus group, but have made it even weirder than ever before.

The evocatively named Pandoraviruses are the new record holders. At 600 nanometres in diameter, they are larger than many species of bacteria and all other viruses on the planet. From freshwater pond mud in Australia came Pandoravirus dulcis and from coastal sediments in Chile came Pandoravirus salinus. The geographical distances and environmental differences between the two groups show that they are actually more common than confined to a highly specialized environment.

 A chart comparing the genetic complexity of the three domains of life with the viruses.
The real surprises came when the genomes of the Pandoraviruses were analysed. They were massive. P. dulcis possessed 1.9 million nucleobases making up around 2500 individual genes. For perspective, humans have around 24,000 genes while something like HIV has just 9 genes. P. salinus was smaller with 2.47 million nucleobases making up 1900 genes. In terms of size and genetic complexity, the Pandoraviruses are within the bounds of free-living prokaryotes (simple cells such a bacteria) and just breach the level of complexity seen in parasitic eukaryotes (complex cells such as a amoeba).

Is is possible that the tree of life has a fourth branch?
At this point we must ask ourselves if the Pandoraviruses should be counted as living organisms. While they are parasitic, they have the level of complexity seen in parasitic eukaryotes and free-living prokaryotes, both of which are considered living organisms. The biggest surprise, however, came when the genes themselves were examined. All living creatures on the planet share a certain number of genes. Some will share more than others depending on when their ancestors split from each other. For example, plants and animals diverged at least 900 million years ago. Even so, we still share 50% of our genes with a banana.

While the number of genes we have in common with bacteria is smaller, it is still significant. Even viruses share some of our most fundamental genes. The Pandoraviruses are completely different. Out of their maximum of 2500 genes, just 7% are found in other viruses and cells. 'Because more than 93% of Pandoraviruses genes resemble nothing known,' write the researchers in the latest issue of Science, 'their origin cannot be traced back to any known cellular lineage. However, their DNA polymerase does cluster with those of other giant DNA viruses

DNA polymerase is the enzyme which splits apart the two halves of a DNA molecule, allowing its information to be read. Slight differences in its structure allow a researcher to identify which domain of life it comes from. Indeed, it was DNA polymerase which allowed Carl Woese to identify the archaea as a group separate to the bacteria. Due to the similarities between the DNA polymerase of giant viruses, the researchers have suggested the controversial existence of a fourth domain of life separate from the bacteria, archaea and eukaryotes, a completely new branch on the tree of life which we previously did no know existed.