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August 11, 2009

Minimal Life: Drawing the line

On the afternoon of the second day of NSF’s Minimal Life workshop, Eric Smith of the Santa Fe Institute in New Mexico provided a much-needed synthesis.

He examined the trade-offs of having a super-pared-down genome and the need to leech off of the environment — parasites, for example, can only survive with bare-bones genomes because they farm out most of their metabolic needs to their hosts. He presented his not surprising, but necessary, quantitative data showing that the more dependent an organism is on its environment, the less metabolically complete its own genome is.

Smith discussed the metabolic and biosynthetic pathways that seem to be universally needed for life, which all involve the same five precursors (the famous CHNOPS from high school chemistry), the same cofactors, and produce pretty much the same amino acid nucleotides. But while it’s hard to find the complete networks for all these necessary bits and pieces at the level of an individual species, they are indeed wrapped into a nice little package at the level of the ecosystem. The boundary between organism and ecosystem, then, is more fluid and less important than most people assume.

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Minimal life: Engineering the simplest life

On the first day's afternoon at the NSF workshop on "minimal life", discussants took an engineering approach to understanding the simplest forms of life. Here, engineers are sort of the “cheaters” of the group — unlike the other scientists, they get to understand the minimum required for life by looking at things that are simpler than what naturally occur in nature.

Clyde Hutchison of the J Craig Venter Institute said the ultimate goal of his work was “a complete description of biological systems in terms of the laws of chemistry and physics.” While physicists have the hydrogen atom as their simple model organism, biologists must use minimal cells. He's not talking about chunky, complicated yeast — his cell of choice is Mycoplasma genitalium, the smallest cell that can be grown independently in the labroatory, and its 580 kb genome, the smallest known genome of any bacterium capable of independent life, he says. And even that's not little enough for his fancy: he wants to see how much of it he can trim away and still have the tiny thing function.

“Are there cells that can live in the lab that are significantly simpler than cells that exist in nature?” he asks.

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Minimal Life: Nature's smallest life

This week at the National Science Foundation headquarters in Arlingon, Virginia, a small group of researchers got together for a workshop about “minimality” in biology. Participants considered the teeniest living cells, the shortest genomes, the simplest engineered systems — basically asking, how low can you go and still have “life”?

The morning sessions on 10 August focused on “unusual life”. Stephen Giovannoni of Oregon State University in Corvallis talked about SAR11, a clade of tiny planktonic bacteria that happen to be the most numerous microorganism in the ocean's uppermost waters. Evolution has done an impressive job trimming the fat from SAR11's genomes — the genome of one member, Pelagibacter ubique, has no introns, extrachromosomal elements, transposons or non-coding genes, and has the shortest between-gene “spacers” known. With only 1.3 million base pairs, its genome is the smallest of any free-living microorganism — although a similar claim was made by almost all the speakers today about their organisms — and makes up 30% of their teeny cell bodies.

Such a barren genetic code means SAR11 is pretty dependent on its environment. It may not be a traditional parasite, in that it isn't constantly sucking the life force of another organism, but it does make you wonder where to draw the line between an organism and its environment. SAR11 depends on seawater for five essential cofactors, as well as for the amino acids glycine and serine. And as reported last year in Nature, it must get reduced sulfur compounds that are made by other plankton.

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