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.

[Rokurota]

Ha!Ha!

My genome is bigger than yours!

[martin_fierro]

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.

"Waiter, there's something dead in my soup. May I have some more?"

[BipolarBob]

I've been trying to lose a little weight and have blamed it on my genes. I think I have too many genes to fit into my jeans. I hope this research pays off and I can shed a few genes.

[Paleo Conservative]

[silverleaf]

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.

Well, I was enjoying the article until the last sentence. Darwin must be sitting at the Right Hand of God as reward for all that hard work of explaining the design.

[Red Badger]

It ain't easy bein' gene.......

[Moral Hazard]

" Well, I was enjoying the article until the last sentence. "

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

[LibWhacker]

ocean water - likens it to a very thin chicken soup

OTOH, now we know we'll never starve because there are five enormous bowls of free chicken soup on the planet! ;-)

[starfish923]

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

No duplicates = no redundancy, that is, no back up system.
I know many humans like this.

[PatrickHenry]

EvolutionPing

A pro-evolution science list with over 300 names. See the list's explanation at my freeper homepage. Then FReepmail to be added or dropped.

[Right Wing Professor]

Here's the genome map if anyone wants to browse. Click anywhere to zoom in; the colored boxes are genes; several contiguous boxes of the same color denote a single RNA transcript; the arrows are the direction of transcription; click on the box to find out what we think the gene codes for.

[Redbob]

If you're overweight, PLEASE don't take off your genes in public!

[ndt]

"My genome is bigger than yours!"

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

[Right Wing Professor]

Correction; the colors code for the metabolic pathway the gene is involved in.

[Alamo-Girl]

Thanks for the ping!

[Aracelis]

Thanks, RWP! Very interesting information!

[PatrickHenry]

Here's the genome map if anyone wants to browse.

It's a code. A code from the Intelligent Designer!! It says: "Twin towers, 9/11 ... Bush did it for the oil."

[LibWhacker]

Very interesting, thanks!

[Sinner6]

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

You should try reverse transcription. WOW!

[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.

[AdmSmith]

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.

Very few bacteria have "junk" DNA or viral genes or duplicate gene copies (probably due to selection pressure), so that is no surprise. "Junk" DNA are of various types and we probably have to live with the use of this term for a long time, even in Science http://www.sciencemag.org/content/vol309/issue5738/twis.shtml .

I wonder when this record (1,354 genes)will be broken; next year?

[Old Professer]

I ain't listening to no peg-legged bacterium.

[contemplator]

..why other genomes have accumulated so much apparently random stuff, if there is some genetic advantage to be gained from this streamlining.

Of course this idea implies some sort of species conciousness going on during the cellular formation stage and will no doubt attract criticism from everyone but hey, wild thoughts have their place too...

As in the case of the whale, in the event that things don't turn out to be as advantageous on land as you would like, you have the ability to revert much faster if you have saved the codes for the appropriate cellular engines. This ability to "devolve" in a rapid fashion might come in handy should your species suddenly need to survive another ice age.

[js1138]

"so many" = all

At least all biologists publishing original research.

[js1138]

I knew there was a practical reason for never throwing anything away.

[AndrewC]

My goodness...

Where is all the "junk" demanded of a "random" unthinking process? Or is any change an immediately fatal one?

[RightWingNilla]

Its not the size of the genome but how you splice it.

[RightWingNilla]

I thought it was typical for prokaryotes to have very streamlined genomes with little/no unused DNA?

[jennyp]

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.

It seems the function is very forceful indeed! I've never heard of a species actually favoring some bases over others because of the incrementally higher metabolic cost:

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.

(me to Pelagibacter: "Dude, that is extreme!"

Something occurs to me: In larger populations, natural selection plays a more significant role than in smaller populations. That's why biologists talk about genetic drift being more significant players in speciation, as the small breakaway population gets isolated from the bigger parent population.

So if these "estimated 20 billion billion billion" Pelagibacters are spread out all across the oceans, that's one huuuuuge population. Neutral mutations would have no chance at all to spread across the population, let alone even a minisculely harmful mutation. So any genetic innovation, which might survive in a small founder population long enough to develop into something positive, would never get the chance to start the experiment.

[LiteKeeper]

YEC INTREP