Scientist Plans to Crack Genetic Secrets of the Deep - From Comfort of His 100ft Yacht

It is hard to think of a more audacious scientific endeavour - to catalogue the genetic diversity of the most abundant living group in the largest habitat on Earth. At the same time, the project will compile a huge genetic library that will teach scientists how living things are put together and help them to harness novel genes for creating new drugs or pollution-free energy.

The driving force behind this, self-styled maverick scientist Craig Venter, is no stranger to audacity. He was vilified by the scientific establishment for taking them on in the race to sequence the human genome. Since an uneasy draw in the genome contest was brokered in 2000 between public and private sequencing efforts, he has been in no mood to rest on his laurels.

His latest project is the Global Ocean Sampling Expedition, carried out by a team of scientists aboard his research yacht Sorcerer II. The aim is to sequence the DNA of micro-organisms in water samples collected at intervals during a circumnavigation of the globe. This is the modern equivalent of Victorian explorers reaching the interior of the African continent and returning with countless bizarre beasts never encountered by western science. Less than 1% of the planet's microbes can be grown in the lab and only a fraction of them have been studied in any detail. The other 99% are virtually unknown.

The team at the J Craig Venter Institute, Dr Venter's not-for-profit research facility in Rockville, Maryland, have already made a sizeable dent in this vast wilderness of ignorance. The scientists have filtered the water to take the microbes out, then sequenced their DNA. So far they have published the sequences of 7.7m individual DNA strands covering 6.3bn DNA letters (roughly twice the size of the human genome). Most remarkably, this vast collection of DNA instructions contains code for more than 6m protein sequences.

Even though many of these are fragments, the haul nearly doubles the number of all known proteins that have been gleaned from sequence data by science before - and so far, the team has only published information from a quarter of its samples. The results, which appear in three papers in the online open access journal the Public Library of Science: Biology, use data from 44 sites down the north-east coast of the US, through the Caribbean and Panama canal, and out to the Galapagos islands in the Pacific. "Instead of being at the end of discovery it means we are at the early stages," said Dr Venter. "We have a long way to go to understand life here."

Dr Venter points out that ocean microbes are perhaps our biggest hope of slowing down or stopping global warming, because the oceans store masses of carbon. "They are largely responsible for the atmosphere we have to breathe," he said. Perhaps the oceans could be seeded with tailor-made communities of micro-organisms that speed up carbon dioxide uptake. "In the longer run, there will be effects on our understanding of a huge array of genes, based on their sequences, with implications for protein engineering," said Gerard Manning, part of Dr Venter's team at the Salk Institute in California.

By seeing the many ways in which a protein can be put together, scientists should have a better idea of how to design new proteins from scratch.

The huge catalogue of new off-the-shelf genes will also be extremely useful. "Truly novel proteins provide a treasure trove that may some day cure cancer, provide ways to produce chemical energy efficiently, or who knows," said team member Douglas Rusch.

Many proteins from micro-organisms are already used in industrial processes, but having different versions which perhaps work at different temperatures or levels of acidity would allow companies to fine-tune these processes or make them less energy-hungry. It will all be useful genetic fodder for another of Dr Venter's pet projects, an attempt to build a synthetic organism from scratch.

Dr Venter's bull-in-a-china-shop entry into human genome sequencing earned him the epithet "bad boy of science" from Time magazine in 2000. Many of his colleagues in the scientific community who condemned his plans to make money from information gleaned from the human genetic code were less polite.

The former high-school dropout's latest scientific endeavour does not attract the same vitriol from rivals. He recalls an incident at university in which a professor told him that biology had been pretty much wrapped up. "I was told it was difficult to make any new discoveries in biology because essentially everything is known," he recalled. His professor had obviously not thought of genomics.

Potential uses


Health

The genes uncovered during the voyages of the Global Ocean Sampling Expedition will provide scientists with numerous potential leads for new drugs. Many of the bacteria in Dr Venter's samples will have developed defences against other bacteria and viruses. These defences could be co-opted for the benefit of patients

Climate

Ocean microbes could be used to mitigate the effects of climate change by soaking up CO2 in the atmosphere. The ocean is the largest sink for CO2

Energy

If their biochemical machinery can be harnessed it may be possible to engineer microbes which, for example, produce hydrogen or convert hydrogen and CO2 into methane