Ocean bug has 'smallest genome'

BBC ^ | 8/19/05 | Roland Pease

[LibWhacker]

Small but perfectly formed, Pelagibacter ubique is a lean machine stripped down to the bare essentials for life.

Humans have around 30,000 genes that determine everything from our eye colour to our sex but Pelagibacter has just 1,354, US biologists report in the journal Science.

What is more, Pelagibacter has none of the genetic clutter that most genomes have accumulated over time.

There are no duplicate gene copies, no viral genes, and no junk DNA.

'Chicken soup'

The spareness of its genome is related to its frugal lifestyle. The shorter the length of DNA that needs to be copied each generation, the less work there is to do.

Pelagibacter has even gone one step further. It has chosen where possible to use genetic letters - or base pairs - which use less nitrogen in their construction: nitrogen is a difficult nutrient for living things to obtain.

The result is one of the most successful organisms on the planet. Pelagibacter feeds off dead organic matter that is dissolved in ocean water - lead researcher Stephen Giovannoni of Oregon State University likens it to a very thin chicken soup.

The dissolved carbon is always there, so there is no need to build in special metabolic circuits to adjust between periods of feast and famine. Indeed, in laboratory studies, the Oregon biologists have found that adding nutrients to the broth has no effect on the microbe's vigour.

Self-sufficient

The sheer abundance of Pelagibacter - there are an estimated 20 billion billion billion Pelagibacter microbes scattered throughout the world's oceans - is probably what has allowed the organism to streamline its genes.

With so many copies in the ocean, there are plenty of opportunities for random mutations to try out more thrifty combinations.

There are organisms with smaller genomes - Mycoplasma genitalium has about 400 genes. But these are all obligate parasites or symbionts, relying on other organisms to do the jobs they have abandoned. Pelagibacter is entirely self-sufficient.

There is a great deal of interest in finding out how few genes a living organism can get away with. Bio-entrepreneur Craig Venter is trying to create an artificial version of a bacterium, aiming for as few as 300 genes.

Stephen Giovannoni says the synthetic one will barely function. But Pelagibacter on the other hand, accounting for a quarter of all organisms in the ocean, is a shining example of Darwin's principle, the survival of the fittest.

[silverleaf]

It's a shame that biologists don't bow to religious orthodoxy apparently

Perhaps so. But perhaps a bigger shame that so many biologists cling so tenaciously to a theory based on Darwin's 19th century understanding of cellular biology...which he himself admitted would completely break down in the event of discovery of irreducible complexity. Thank God medical science didn't stop in 1859.

[Servant of the 9]

What is more, Pelagibacter has none of the genetic clutter that most genomes have accumulated over time.

There are no duplicate gene copies, no viral genes, and no junk DNA.

If every creature was this elegantly put together, there might, might, be a case for Inteligent Design.

As things are, there isn't.

So9

[Right Wing Professor]

Thank you. Fascinating organism, and I hadn't heard about it.

[Moral Hazard]

"But perhaps a bigger shame that so many biologists cling so tenaciously to a theory based on Darwin's 19th century understanding of cellular biology..."

So they're stupid and you know better than they do?

[contemplator]

entrepreneur Craig Venter is trying to create an artificial version of a bacterium, aiming for as few as 300 genes.

Cue the Dr. Frankenstein voice saying "It's alive!"

[Rokurota]

It's not the size of the genome but how you transcribe it.

Could you translate that for me?

[ndt]

"Could you translate that for me?"

If I did I would be banned, it's bad genome sex humor.

[trubluolyguy]

Am I the only one that ever wonders WHY we need this information?

[Rokurota]

Am I the only one that ever wonders WHY we need this information?

Because it is one step closer to creating a race of pig-men.

[Clemenza]

The government has been experimenting with Pig Men for years!

[Southack]

"There are no duplicate gene copies, no viral genes, and no junk DNA."

All this time...and no viral genes are in its DNA!

My goodness...

[r9etb]

If every creature was this elegantly put together, there might, might, be a case for Inteligent Design. As things are, there isn't.

Perhaps. But given the "it's thriftiest" explanation provided for this "very clean" genome, I think it raises a number of very significant questions with regard to why other genomes have accumulated so much apparently random stuff, if there is some genetic advantage to be gained from this streamlining.

The thing that comes to my mind is: maybe that "random stuff" isn't really random after all, but simply serves some purpose we haven't discovered yet.

[balrog666]

You should try reverse transcription. WOW!

You're sick! Sick! ;^)

[furball4paws]

I am a little familiar with this bug and I knew they were sequencing it. I am not surprised at its size. It has paid the price of not being able to respond to local environmental excesses by adapting to a very thin soup.

BTW, open ocean is P limited not N, but combined N is still difficult to find. I rather doubt the 25% number. All in all a good find and thanks for the link too!

[jennyp]

But given the "it's thriftiest" explanation provided for this "very clean" genome, I think it raises a number of very significant questions with regard to why other genomes have accumulated so much apparently random stuff, if there is some genetic advantage to be gained from this streamlining.

The thing that comes to my mind is: maybe that "random stuff" isn't really random after all, but simply serves some purpose we haven't discovered yet.

Well, at least some of the random stuff has been proven to be useless to survival. They bred knockout mice, where the knocked out regions were noncoding regions of no previously known function. The mice were indistinguishable from normal mice. I don't know if they ever tried to breed a line of mice from those knockout mice, so I don't know if there are any long-term effects to knocking out that particular line of junk, but it's still rather compelling evidence that much of the noncoding sequences really ARE junk DNA.

Some scientists have speculated that pseudogenes, at least, form a junkyard like those in Junkyard Wars: They provide lots of ready-made subassemblies that can be pressed into service later on.

Then there's the rationale I've thought of for having junk DNA: When a gene duplicates, it gets plopped down in a (presumably) random spot on some chromosome. If there was no junk DNA, then the chance would be 100% that the duplicated gene would "crash" into another already-functioning gene, most likely disabling it. With 95% of our genome being junk, there's only a 5% chance that a gene duplication would disable a currently functioning gene.

So when a genome acquires the capability to produce stretches of junk DNA, it's actually acquiring a buffer zone that acts synergistically to vastly increase the viability of gene duplication as an evolutionary tool.

I think the JennyP Theory of Noncoding DNA explains why most single-celled organisms don't have junk DNA while all(?) multicelled organisms do.

[Dimensio]

But perhaps a bigger shame that so many biologists cling so tenaciously to a theory based on Darwin's 19th century understanding of cellular biology...which he himself admitted would completely break down in the event of discovery of irreducible complexity.

What biologists are still doing this, and what's this about "irreducible complexity"?

[PatrickHenry]

I think the JennyP Theory of Noncoding DNA explains why most single-celled organisms don't have junk DNA while all(?) multicelled organisms do.

Not bad at all.

[zeugma]

Some scientists have speculated that pseudogenes, at least, form a junkyard like those in Junkyard Wars: They provide lots of ready-made subassemblies that can be pressed into service later on.

I tend to lean in this direction. It seems to me that G-d isn't doesn't leave a lot of extra stuff laying around for no reason. Perhaps they had a function in the past that was superceded by changing needs and/or conditions. DNA is truely wonderous stuff, and a very efficient way of storing a lot of information.

[aimhigh]

The thing that comes to my mind is: maybe that "random stuff" isn't really random after all, but simply serves some purpose we haven't discovered yet.

I absolutely agree. Medical science has always been quick to dismiss anything they don't understand. Medical science still understands very little about the complexities of the human body. There's a small genetic deletion called VCFS (22q11.2), which can result in 180 different medical problems.

[r9etb]

I don't know if they ever tried to breed a line of mice from those knockout mice, so I don't know if there are any long-term effects to knocking out that particular line of junk, but it's still rather compelling evidence that much of the noncoding sequences really ARE junk DNA.

OTOH, how many times have we recently seen announcements about scientists who've discovered that sections previously thought to be junk, were really used for something?

It seems more than a bit premature to speculate that what we don't understand is "junk until proven otherwise."

As for the JennyP theory, that's part of what I was getting at: if there's a forcing function toward "thriftiness," it seems that the accumulation of "buffers" in the middle of a genome shouldn't happen.