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Ocean bug has 'smallest genome'
BBC ^ | 8/19/05 | Roland Pease

Posted on 08/19/2005 9:44:18 AM PDT by 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.


TOPICS: News/Current Events
KEYWORDS: bug; crevolist; dna; genes; genetic; genome; microbe; nitrogen; ocean; pelagibacter; smallest
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To: LibWhacker
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?
41 posted on 08/19/2005 12:55:19 PM PDT by AdmSmith
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To: LibWhacker

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


42 posted on 08/19/2005 12:58:36 PM PDT by Old Professer (As darkness is the absence of light, evil is the absence of good; innocence is blind.)
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To: r9etb
..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.
43 posted on 08/19/2005 1:05:19 PM PDT by contemplator (Capitalism gets no Rock Concerts)
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To: Moral Hazard

"so many" = all

At least all biologists publishing original research.


44 posted on 08/19/2005 3:28:22 PM PDT by js1138 (Science has it all: the fun of being still, paying attention, writing down numbers...)
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To: jennyp

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


45 posted on 08/19/2005 3:32:51 PM PDT by js1138 (Science has it all: the fun of being still, paying attention, writing down numbers...)
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To: Southack
My goodness...

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

46 posted on 08/19/2005 4:43:13 PM PDT by AndrewC (Darwinian logic -- It is just-so if it is just-so)
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To: ndt
Its not the size of the genome but how you splice it.
47 posted on 08/19/2005 5:42:19 PM PDT by RightWingNilla
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To: furball4paws

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


48 posted on 08/19/2005 5:44:20 PM PDT by RightWingNilla
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To: r9etb
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.

49 posted on 08/19/2005 6:00:52 PM PDT by jennyp (WHAT I'M READING NOW: my post)
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To: LibWhacker

YEC INTREP


50 posted on 08/19/2005 6:16:57 PM PDT by LiteKeeper (The radical secularization of America is happening)
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To: RightWingNilla
The way you define things is of importance here. Procaryotes are certainly much more streamlined and have, typically, some "junk DNA" (is it really "junk"?).

However, some bacteria carry incredible amounts of baggage. Some Pseudomonas species can use over 200 different chemicals as sole source of carbon and energy. That entails carrying a number of genes around in good operating order should one run into one of these compounds that is rarely available. Other bacteria like Pelagibacter are highly specific and carry little extra information.

Two different solutions to life's problems. One adapts to eating a dilute soup that's unlikely to change (at least rapidly) and that there is a lot of. The other is able to adapt quickly to an influx of just about any carbon and energy source, but carries a lot of excess baggage in order to do it.

51 posted on 08/20/2005 12:44:18 PM PDT by furball4paws (One of the last Evil Geniuses, or the first of their return.)
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To: jennyp

"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."

IOW it's setting itself up for extinction?


52 posted on 08/20/2005 12:46:21 PM PDT by furball4paws (One of the last Evil Geniuses, or the first of their return.)
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To: furball4paws
"...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."

IOW it's setting itself up for extinction?

I dunno about that. But natural selection is more dominant in large populations than in small ones, and so it overwhelms the action of genetic drift.

So I think they're not setting themselves up for extinction, but they are preventing themselves from ever making any major evolutionary changes. They'll always remain nothing more than the best Pelagibacters they can possibly be.

53 posted on 08/22/2005 12:02:04 PM PDT by jennyp (WHAT I'M READING NOW: my post)
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