Ua Researchers Find Smallest Cellular Genome

[Reverend AtheiStar]

http://www.eurekalert.org/pub_releases/200...a-urf100606.php

 

UA researchers find smallest cellular genome

 

The smallest collection of genes ever found for a cellular organism comes from tiny symbiotic bacteria that live inside special cells inside a small insect.

 

The bacteria Carsonella ruddii has the fewest genes of any cell. The bacteria's newly sequenced genome, the complete set of DNA for the organism, is only one-third the size of the previously reported "smallest" cellular genome.

 

"It's the smallest genome -- not by a bit but by a long way," said co-author Nancy A. Moran, UA Regents' Professor of ecology and evolutionary biology and a member of the National Academy of Sciences. "It's very surprising. It's unbelievable, really. We would not have predicted such a small size. It's believed that more genes are required for a cell to work."

 

Carsonella ruddii has only 159,662 base-pairs of DNA, which translates to only 182 protein-coding genes, reports a team of scientists from The University of Arizona in Tucson and from Japan.

 

The finding provides new insights into bacterial evolution, the scientists write in the Oct. 13 issue of the journal Science.

 

Atsushi Nakabachi, a postdoctoral research associate in UA's department of ecology and evolutionary biology and a visiting scientist at RIKEN in Wako, Japan, is the first author on the research report, "The 160-kilobase genome of the bacterial endosymbiont Carsonella." The research was conducted in senior author Masahira Hattori's laboratory in Japan and in Moran's lab at the UA.

 

A complete list of authors is at the bottom of this release. The Ministry of Education, Culture, Sports, Science and Technology of Japan funded the work.

 

Many insects feed on plant sap, a nutrient-poor diet. To get a balanced diet, some sap-feeders rely on resident bacteria. The bacteria manufacture essential nutrients, particularly amino acids, and share the goodies with their hosts.

 

In many such associations, the bacteria live within the insect's cells and cannot survive on their own. Often the insect host cannot survive without its bacteria, known as endosymbionts.

 

The relationship between some insects and their endosymbionts is so close and so ancient that the insects house their resident bacteria in special cells called bacteriocytes within specialized structures called bacteriomes.

 

Studying the genomes of such endosymbionts can provide clues to how microorganisms' metabolic capabilities contribute to both their hosts and to biological communities.

 

An organism's genome, its complete complement of DNA, provides the operating instructions for everything the organism needs to do to survive and reproduce.

 

Endosymbiotic bacteria live in an extremely sheltered world and have a pared-down lifestyle, so they need a simpler set of instructions. Many of the metabolic pathways that free-living bacteria maintain have been lost after so many generations of living within insects.

 

Nakabachi and Hattori were interested in sequencing the genome of the bacteria Carsonella.

 

Moran had done some previous work on the Carsonella genome and found its DNA composition and evolution to be unusual. She suggested the team pursue the Carsonella that lived inside an Arizona psyllid insect called Pachypsylla venusta. The insect has only one species of endosymbiotic bacteria, which would simplify the genomic analysis.

 

The researchers collected Pachypsylla venusta psyllids from hackberry trees (Celtis reticulata) on the UA campus and around Tucson. The team extracted the Carsonella DNA and sequenced it.

 

Even though endosymbionts need fewer operating instructions to survive, the bacteria's itsy bitsy genome was a surprise.

 

"It lost genes that are considered absolutely necessary. Trying to explain it will probably help reveal how cells can work," said Moran, who is a member of UA's BIO5 Institute.

 

The scientists speculate that in the bacteria's evolutionary past, some of its genes were transferred into the insect's genome, allowing the insect to make some of the metabolites the bacteria needed. Once the insect shouldered those responsibilities and provided the bacteria with those metabolites, the bacteria lost those genes.

 

Animal and plant cells have specialized structures inside them called organelles that are derived from symbiotic bacteria that became incorporated into the cell over the course of evolution.

 

Carsonella's stripped-down genome may indicate that it is on its way to becoming an organelle, the researchers write in their article.

 

 

###

Authors on the paper are:

 

Atsushi Nakabachi of the UA and RIKEN; Helen E. Dunbar and Nancy A. Moran of the UA; Atsushi Yamashita and Hidehiro Toh of Kitasato University in Sagamihara, Japan; Hajime Ishikawa of The University of the Air in Mihama, Japan; and Masahira Hattori of The University of Tokyo in Kashiwa, Japan and RIKEN Genomic Sciences Center in Yokohama, Japan.

 

Contact information:

 

Nancy Moran, 520-621-3581, nmoran@email.arizona.edu

 

Atsushi Nakabachi, bachi@email.arizona.edu, bachi@riken.jp

 

Masahira Hattori, hattori@k.u-tokyo.ac.jp, hattori@gsc.riken.jp

 

Related Web sites:

 

The Moran Laboratory, http://eebweb.arizona.edu/faculty/moran/

 

The Hattori Laboratory, http://genome.ls.kitasato-u.ac.jp/

[HuaiDan]

I forget many of the specifics, but interesting to note that mitochondria (the energy producing organelles in all living cells) are theorized to have arisen from ancient free-living bacteria.

And don't mitochondria have their own independent genome apart from the 'host' organism? What exactly would be the distinction between a mitochondria and the microorganism cited above, as they both can not live independently of the organism they reside in?

[Piprus]

I forget many of the specifics, but interesting to note that mitochondria (the energy producing organelles in all living cells) are theorized to have arisen from ancient free-living bacteria.

And don't mitochondria have their own independent genome apart from the 'host' organism? What exactly would be the distinction between a mitochondria and the microorganism cited above, as they both can not live independently of the organism they reside in?

The mitochondria are intracellular structures that carry out the energy production within the cell by a series of biochemical transformations that release energy-rich compounds like ATP. They're called the "power units" of the cell. In contrast, a symbiotic organism such as the one mentioned above lives with the host in a "give and take" relationship. In return for the host providing something such as a substrate (food) the bacteria lives on, the bacteria gives back a benefit such as a necessary enzyme or other metabolic need to the host. Our own human bowels are loaded with symbiotic bacteria we call the "intestinal flora".

 

So, mitochondria are structures within a cell, whereas bacteria are cellular organisms themselves.

[HuaiDan]

In return for the host providing something such as a substrate (food) the bacteria lives on, the bacteria gives back a benefit such as a necessary enzyme or other metabolic need to the host.

 

So how does that vastly differ from the relationship between the mitochondria and the cell it resides in?

[Callyn]

In return for the host providing something such as a substrate (food) the bacteria lives on, the bacteria gives back a benefit such as a necessary enzyme or other metabolic need to the host.

 

So how does that vastly differ from the relationship between the mitochondria and the cell it resides in?

Mitochondria contain only a portion of their DNA, the rest having moved to the nucleus. Also, it sounds as if these bacteria make their own energy and carry out all life processes by themselves, while mitochondria perform only one function within the cell.

[Amanda]

Hi Reverend! Great article, as usual!

 

Reading this article initially, I thought it might lend some insights to abiogenesis because:

 

In many such associations, the bacteria live within the insect's cells and cannot survive on their own. Often the insect host cannot survive without its bacteria, known as endosymbionts.

 

I thought maybe in evolution, two components that could not function on their own, that were confined and associated with other components having a mutually complimentary symbiotic relationship, however, not within each other but along side of each, and as evolution would have it, they could have eventually merged to make a self sufficient living organism. Then I read this:

 

Endosymbiotic bacteria live in an extremely sheltered world and have a pared-down lifestyle, so they need a simpler set of instructions. Many of the metabolic pathways that free-living bacteria maintain have been lost after so many generations of living within insects.

 

Now, I realize that 'endosymbionts' are not considered just engaged in the symbiotic relationship between two orgainisms, but that it is more depended on being inside its host and downsizing its systems deemed as no longer necessary. Don't you think this insight of something such as isolated endosymbiotic forms evolving a symbiotic relationships, could have been merging along side of others to have been the precursors to life?

[Reverend AtheiStar]

Hi Reverend! Great article, as usual!

 

Reading this article initially, I thought it might lend some insights to abiogenesis because:

 

In many such associations, the bacteria live within the insect's cells and cannot survive on their own. Often the insect host cannot survive without its bacteria, known as endosymbionts.

 

I thought maybe in evolution, two components that could not function on their own, that were confined and associated with other components having a mutually complimentary symbiotic relationship, however, not within each other but along side of each, and as evolution would have it, they could have eventually merged to make a self sufficient living organism. Then I read this:

 

Endosymbiotic bacteria live in an extremely sheltered world and have a pared-down lifestyle, so they need a simpler set of instructions. Many of the metabolic pathways that free-living bacteria maintain have been lost after so many generations of living within insects.

 

Now, I realize that 'endosymbionts' are not considered just engaged in the symbiotic relationship between two orgainisms, but that it is more depended on being inside its host and downsizing its systems deemed as no longer necessary. Don't you think this insight of something such as isolated endosymbiotic forms evolving a symbiotic relationships, could have been merging along side of others to have been the precursors to life?

 

Life would have to have evolved first for any symbiosis between two life forms to occur. I like to look at viruses as a model of how pre-life might have looked like -- minus the invasion of a host, of course. Just look at them. They're like microscopic robots! They don't grow, they don't eat, they don't breathe! How freaky is that? That is precisely what a self-replicator would be like.

 

Here's a pic of my all time favorite virus. It has the coolest shape of anything that small:

 

[Amanda]

Life would have to have evolved first for any symbiosis between two life forms to occur. I like to look at viruses as a model of how pre-life might have looked like -- minus the invasion of a host, of course. Just look at them. They're like microscopic robots! They don't grow, they don't eat, they don't breathe! How freaky is that? That is precisely what a self-replicator would be like.

 

Hey Reverend! I thought abiogenesis is a theory that chemicals coalescing in some sort of confined area, in the primordial soup, probably with amino acids, perhaps stimulated by lightning, had symbiotic catalytic effects on each other… suggesting the precursor to life. Now, if there were different aggregates of separate and different composites of this activity that complimented and supported each other, evolving to merge with each other, and similar ones merging again with each other, till we finally have self replicating polypeptide chains, mRNA, then the appearance of DNA, then a living organism!

 

I like your image of a bacteriophage, as it looks quite scifi! However, if it does not eat, nor grow, doesn’t that contradict the requirements to be considered life? I see it has proteins and DNA, but how can it get energy without breathing or eating? Also, isn’t that still a bit complex to be the initial life form? Don’t you think the original life form was probably energized by some sort of osmotic consumption?

 

Also, I don‘t know what bacterophages are, but saw where they infect other bacteria! Is that a good thing to have something like E. coli infected? Does that then mean E. coli dies?

[Reverend AtheiStar]

I like your image of a bacteriophage, as it looks quite scifi! However, if it does not eat, nor grow, doesn’t that contradict the requirements to be considered life?

 

Sure does. This is why I said it resembles what pre-life might have looked like.

 

I see it has proteins and DNA, but how can it get energy without breathing or eating?

 

Viruses don't need to do anything but dock with a cell and inject it's DNA. I would think this could be accomplished without the need for any additional energy input (beyond what was put in in the form of potential energy when it was produced inside the host cell) required. How, exactly is another matter. I think I'll have to do some research.

 

Also, isn’t that still a bit complex to be the initial life form?

 

We're talking about pre-life, not life. But yes, it's still too complex to be even that. This is why I was saying it resembled what pre-life must have looked like. As in, it doesn't qualify as living and its primary goal is to replicate.

 

Don’t you think the original life form was probably energized by some sort of osmotic consumption?

 

Yes. Although I'm sure that moving on to eating other organisms wouldn't take long -- if it wasn't there from the beginning.

 

Also, I don‘t know what bacterophages are, but saw where they infect other bacteria! Is that a good thing to have something like E. coli infected? Does that then mean E. coli dies?

 

Yes. Generally when a cell explodes from the inside, death is the result!

[Amanda]

 

 

Aha! Reverend Atheistar, thanks for the wonderful lesson of enlightenment!

 

Now I see why you think a simpler form of bacteriophage could have been a precursor to life. Maybe it met with something else that complimented its structure, went into it, and the two made life? I suppose a mitochodrial aspect is a bit complex to have been close to the initial onset of life too?

[Reverend AtheiStar]

 

 

Aha! Reverend Atheistar, thanks for the wonderful lesson of enlightenment!

 

Now I see why you think a simpler form of bacteriophage could have been a precursor to life. Maybe it met with something else that complimented its structure, went into it, and the two made life? I suppose a mitochodrial aspect is a bit complex to have been close to the initial onset of life too?

 

You're welcome. I'm glad I could help you.

 

That is possible, yes. It seems unrealistic, though. I think that the pre-life was a simple replicator that didn't need a host and lacked the capability to do so, anyway. All it could do was make copies of itself. Through this simple form of reproduction, complexity grew and it eventaully led to something we would call alive.

 

Mtichondria are believed to have been independent cells at one point. This would mean they'd have to been living. This rules them out as being pre-life. Here's a great article I found on the subject:

 

http://www.cod.edu/people/faculty/fancher/LifeTog.htm

 

Life Together: The Origin of Mitochondria and Chloroplasts

 

One of the interesting questions about the history of life is the question of where eukaryotic cells came from. Our fossil record shows us pretty clearly that for the first couple of billion years of the existence of life, all of Earth's life forms were prokaryotic. So where did eukaryotic cells come from?

 

An initial question might be why eukaryotic cells arose. Problems like this rarely have real answers – just good ideas. One important thing that changed in the world about the time that the first eukaryotic fossils appear is that the atmosphere of the planet was beginning to fill up with free oxygen, almost certainly due to the increasing numbers of photosynthesizing organisms in the world. (Photosynthesis produces oxygen as a waste product). The introduction of significant oxygen into the environment would have initially been a disaster for most life forms of the times, since organisms that live without oxygen (anaerobic organisms) are poisoned by oxygen, which is frankly a very destructive substance. However, those organisms that survived the introduction of oxygen (because they were lucky enough to be able to perform some kind of chemical process that would use up oxygen, thus preventing it from messing around with the vital chemistry of the cell) got a bonus. Oxydation chemistry tends to release energy. So we're pretty sure that it was about this time than aerobic cellular respiration arose. The overwhelming difference between anaerobic cellular respiration and aerobic cellular respiration is the amount of energy produced by the two processes. Aerobic respiration produces many times more energy than anaerobic respiration does. Hypothetically, this increase in available energy was at least part of what promoted the development of the much larger and more complex eukaryotic cell.

 

So where did all of the new structures in eukaryotic cells come from? The probable answer is that there were at least two different kinds of events that added to the complexity of cell structure. Many of the structures in eukaryotic cells probably developed from the elaboration of the membranes of the cell. This is the likely explanation for the origin of the endoplasmic reticulum, golgi apparatus, and nuclear envelope. But the evidence strongly suggests a much more interesting origin for the two great energy processing organelles, the mitochondrion and the chloroplast. These two structures probably arose through a process known as endosymbiosis. [endo=inside; sym=together; bio=life]

 

Symbiosis is a dependent relationship between two organisms. There are three basic kinds: parasitism, in which one partner (the parasite) benefits and the other (the host) is harmed; commensalism, in which one partner (the commensal) benefits and the other partner (the host) is indifferent, and mutualism, in which both partners benefit. These three states are evolutionarily related to each other: parasitic relationships tend to evolve into commensalistic relationships, and commensalistic relationships tend to evolve into mutualistic relationships. This makes perfect sense. Any accidental genetic change in the host which reduces the harm (or causes benefit) from the parasite would certainly be favored by selection; any accidental genetic change in the parasite which keeps its host, upon which it depends, healthy and alive longer would also be favored. So the selective pressure on both sides is toward less and less damage to the host.

 

Endosymbiosis is a symbiotic relationship between two organisms in which one of the organisms lives inside the other. The relationship can be any of the three types of symbiosis. A frequent trend in endosymbiotic relationships is for the endosymbiont – the one inside – to become more and more specialized (and thus dependent upon the host). Endosymbiotic relationships are extremely common; there are endosymbionts living inside your body at this very moment.

 

Almost all biologists believe that this phenomenon explains where mitochondria and chloroplasts came from. Not all organisms developed the ability to perform photosynthesis, or to convert to aerobic cellular respiration. Many of those that didn't make these alterations themselves went into partnership with other organisms that did. If an anaerobic cell could engulf an aerobic one (without digesting it), it could get the benefit of the ATP overflow from its captive partner. Given a couple of billion years to get used to each other, the inside, aerobic partner became so specialized for aerobic cellular respiration that it lost almost all of the basic life skills, depending upon the external host cell to support it. Voila` – mitochondrion. If you tell the same story, but substitute "photosynthesis" for "aerobic cellular respiration," you have a recipe for the invention of chloroplasts.

 

This is an interesting story, but pretty outrageous unless there's some evidence that indicates that it might be true. Glad that you asked ;^)

 

There are some very interesting things about mitochondria and chloroplasts that have had biologists scratching their heads for quite a while. For one thing, both of these organelles have their own DNA molecules. Their DNAs are not duplicates of nuclear DNA – they are exclusive to the mitochondrion or the chloroplast. Mitochondrial DNA carries genes necessary to produce some of the molecules vital for the aerobic respiration process, and chloroplast DNA carries the genes for substances necessary for photosynthesis. The nuclear genes can't duplicate these. Unlike the DNA in the nucleus, mitochondrial and chloroplast DNAs are naked and circular – just like a prokaryotic cell's DNA. These two organelles also have their own ribosomes – and they are different from the ribosomes out in the cytoplasm. The proteins coded for by the mitochondrial genes are produced by mitochondrial ribosomes, and those coded for by the chloroplast genes are produced by chloroplast ribosomes.

 

Another interesting aspect of mitochondrial function is that not all parts of cellular respiration occur in the mitochondria. Aerobic cellular respiration has three parts, but only the second and the third require the presence of oxygen. The first part of cellular respiration (called glycolysis) requires no oxygen, and takes place not in the mitochondria, but out in the cytoplasm of the cell. It is identical to the anaerobic cellular respiration which occurs in cells which cannot use oxygen.

 

There are two very interesting conclusions to draw from these pieces of information. First, these observations strongly suggest that a mitochondrion or chloroplast is very much like a highly specialized and simplified cell living inside a larger cell. Second, it looks very much like the process of aerobic cellular respiration arose as an "add on" process. The aerobic process performed by the mitochondrion were tacked onto the end of the older, anaerobic respiration process.

[Reverend AtheiStar]

I just found this cool pic on the Institute for Molecular Virology in a section they call Virus World:

 

[Amanda]

There are two very interesting conclusions to draw from these pieces of information. First, these observations strongly suggest that a mitochondrion or chloroplast is very much like a highly specialized and simplified cell living inside a larger cell. Second, it looks very much like the process of aerobic cellular respiration arose as an "add on" process. The aerobic process performed by the mitochondrion were tacked onto the end of the older, anaerobic respiration process.

 

Hey Reverend, thanks for the huge insights... AGAIN. It seems these endosymbionts may not have actually been the precursors of life, however, as suggested by this mitochondrial theory... it probably played a significant part in the basic stages of life's evolution.

 

I'm not going to ask you any more questions on this, because you remind me of when I read Scientific American. The initial part of the article is written really simple, interesting, and in layman terms. As I read more and more, it gets more and more complex, till it is over my head. After reading your last post to me... it is getting way over my head! Maybe I can discuss it more if I happen to learn a whole lot more.

[Reverend AtheiStar]

Hey Reverend, thanks for the huge insights... AGAIN. It seems these endosymbionts may not have actually been the precursors of life, however, as suggested by this mitochondrial theory... it probably played a significant part in the basic stages of life's evolution.

 

I'm not going to ask you any more questions on this, because you remind me of when I read Scientific American. The initial part of the article is written really simple, interesting, and in layman terms. As I read more and more, it gets more and more complex, till it is over my head. After reading your last post to me... it is getting way over my head! Maybe I can discuss it more if I happen to learn a whole lot more.

 

lol... Ok, well then I can only tell you three things: read, read, read!!!