First functional 'designer' chromosome synthesized in yeast

Mar 27, 2014
The chromosome is represented snake-like, with the positions of "designer changes" indicated by pins and white diamonds, and the deleted segments indicated in yellow, using the native chromosome sequence as a reference. The approximate position of nucleosomes (protein "packaging" for the DNA in the chromosome) are indicated by the small dots in the center of the chromosome. The positions of the changes are roughly to scale. Credit: Lucy Reading-Ikkanda

An international team of scientists led by Jef Boeke, PhD, director of NYU Langone Medical Center's Institute for Systems Genetics, has synthesized the first functional chromosome in yeast, an important step in the emerging field of synthetic biology, designing microorganisms to produce novel medicines, raw materials for food, and biofuels.

Over the last five years, scientists have built bacterial chromosomes and viral DNA, but this is the first report of an entire eukaryotic chromosome, the threadlike structure that carries genes in the nucleus of all plant and animal cells, built from scratch. Researchers say their team's global effort also marks one of the most significant advances in yeast genetics since 1996, when scientists initially mapped out yeast's entire DNA code, or genetic blueprint.

"Our research moves the needle in synthetic biology from theory to reality," says Dr. Boeke, a pioneer in synthetic biology who recently joined NYU Langone from Johns Hopkins University.

"This work represents the biggest step yet in an international effort to construct the full genome of synthetic yeast," says Dr. Boeke.

"It is the most extensively altered chromosome ever built. But the milestone that really counts is integrating it into a living yeast cell. We have shown that yeast cells carrying this synthetic chromosome are remarkably normal. They behave almost identically to wild yeast cells, only they now possess new capabilities and can do things that wild yeast cannot."

In this week's issue of Science online March 27, the team reports how, using computer-aided design, they built a fully functioning chromosome, which they call synIII, and successfully incorporated it into brewer's yeast, known scientifically as Saccharomyces cerevisiae.

The seven-year effort to construct synIII tied together some 273, 871 base pairs of DNA, shorter than its native yeast counterpart, which has 316,667 base pairs. Dr. Boeke and his team made more than 500 alterations to its genetic base, removing repeating sections of some 47,841 DNA base pairs, deemed unnecessary to chromosome reproduction and growth. Also removed was what is popularly termed junk DNA, including base pairs known not to encode for any particular proteins, and "jumping gene" segments known to randomly move around and introduce mutations. Other sets of base pairs were added or altered to enable researchers to tag DNA as synthetic or native, and to delete or move genes on synIII.

"When you change the genome you're gambling. One wrong change can kill the cell," says Dr. Boeke. "We have made over 50,000 changes to the DNA code in the chromosome and our yeast still live. That is remarkable. It shows that our synthetic chromosome is hardy, and it endows the yeast with new properties."

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An interview about the research with Dr. Jef D. Boeke. Credit: NYU Langone Medical Center, 2014

The Herculean effort was aided by some 60 undergraduate students enrolled in the "Build a Genome" project, founded by Dr. Boeke at Johns Hopkins. The students pieced together short snippets of the synthetic DNA into stretches of 750 to 1,000 base pairs or more, an effort led by Srinivasan Chandrasegaran, PhD, a professor at Johns Hopkins. Chandrasegaran is also the senior investigator of the team's studies on synIII.

Student participation kicked off what has become an international effort, called Sc2.0 for short, in which several academic researchers have partnered to reconstruct the entire yeast genome, including collaborators at universities in China, Australia, Singapore, the United Kingdom, and elsewhere in the U.S.

Yeast chromosome III was selected for synthesis because it is among the smallest of the 16 yeast chromosomes and controls how yeast cells mate and undergo genetic change. DNA comprises four letter-designated base macromolecules strung together in matching sets, or base pairs, in a pattern of repeating letters. "A" stands for adenine, paired with "T" for thymine; and "C" represents cysteine, paired with "G" for guanine. When stacked, these base pairs form a helical structure of DNA resembling a twisted ladder.

Yeast shares roughly a third of its 6,000 genes—functional units of chromosomal DNA for encoding proteins—with humans. The team was able to manipulate large sections of yeast DNA without compromising chromosomal viability and function using a so-called scrambling technique that allowed the scientists to shuffle genes like a deck of cards, where each gene is a card. "We can pull together any group of cards, shuffle the order and make millions and millions of different decks, all in one small tube of yeast," Dr. Boeke says. "Now that we can shuffle the genomic deck, it will allow us to ask, can we make a deck of cards with a better hand for making yeast survive under any of a multitude of conditions, such as tolerating higher alcohol levels."

Using the scrambling technique, researchers say they will be able to more quickly develop synthetic strains of yeast that could be used in the manufacture of rare medicines, such as artemisinin for malaria, or in the production of certain vaccines, including the vaccine for hepatitis B, which is derived from yeast. Synthetic yeast, they say, could also be used to bolster development of more efficient biofuels, such as alcohol, butanol, and biodiesel.

The study will also likely spur laboratory investigations into specific gene function and interactions between genes, adds Dr. Boeke, in an effort to understand how whole networks of genes specify individual biological behaviors.

Their initial success rebuilding a functioning chromosome will likely lead to the construction of other yeast chromosomes (yeast has a total of 16 chromosomes, compared to humans' 23 pairs), and move genetic research one step closer to constructing the organism's entire functioning genome, says Dr. Boeke.

Dr. Boeke says the international team's next steps involve synthesizing larger , faster and cheaper. His team, with further support from Build a Genome students, is already working on assembling base pairs in chunks of more than 10,000 . They also plan studies of synIII where they scramble the chromosome, removing, duplicating, or changing gene order.

Detailing the Landmark Research Process

Before testing the scrambling technique, researchers first assessed synIII's reproductive fitness, comparing its growth and viability in its unscrambled from—from a single cell to a colony of many cells—with that of native yeast III. Yeast proliferation was gauged under 19 different environmental conditions, including changes in temperature, acidity, and hydrogen peroxide, a DNA-damaging chemical. Growth rates remained the same for all but one condition.

Further tests of unscrambled synIII, involving some 30 different colonies after 125 cell divisions, showed that its genetic structure remained intact as it reproduced. According to Dr. Boeke, individual chromosome loss of one in a million cell divisions is normal as cells divide. Chromosome loss rates for synIII were only marginally higher than for native III.

To test the scrambling technique, researchers successfully converted a non-mating cell with synIII to a cell that could mate by eliminating the gene that prevented it from mating.

Explore further: Cell division finding could boost understanding of cancer

More information: "Total Synthesis of a Functional Designer Eukaryotic Chromosome," by N. Annaluru et al. Science, 2014.

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Returners
1 / 5 (1) Mar 27, 2014
and "C" represents cysteine, paired with "G" for guanine. When stacked, these base pairs form a helical structure of DNA resembling a twisted ladder.


That's Cytosine.

How could you make that mistake?
tekram
3 / 5 (2) Mar 27, 2014
..That's Cytosine.

How could you make that mistake?

Contact: David March
Senior Public Relations Specialist
david.march@nyumc.org

David wasn't paying attention in class. That is why he is in public relations.

betterexists
1 / 5 (1) Mar 27, 2014
Certainly GREAT! Beats Obokata's stuff unless she is not doing April Fool of Everyone. Her Harvard Boss is still behind her! We will know Pretty Pretty Pretty SOON!
betterexists
1 / 5 (1) Mar 27, 2014
Why NOT mess up DNA of Neotenic Axolotl larvae at their zygote level?
They can make 1000s of varieties of them....containing series of changes..from 1 or 2 changes to more & more!
Then, we can see when, why and how REGENERATION of it stops or gets enhanced.
Regeneration is THE MOST Important Field AFTER Ageing.
Not only an individual is losing parts of the body one is born with.....Society also is losing Most Accomplished Humans.
IT IS HIGHLY IMPERATIVE that both losses should be halted ASAP.
Once Energy is made easily available with Nuclear Fission or some Biofuel....The Planet OR our Solar System CAN tolerate the BURDEN of the Increased Populations!
betterexists
1 / 5 (1) Mar 27, 2014
Read on wikipedia website:
"The feature of the salamander that attracts most attention is its healing ability: the axolotl does not heal by scarring and is capable of the regeneration of entire lost appendages in a period of months, and, in certain cases, more vital structures. Some have indeed been found restoring the less vital parts of their brains. They can also readily accept transplants from other individuals, including eyes and parts of the brain—restoring these alien organs to full functionality. In some cases, axolotls have been known to repair a damaged limb, as well as regenerating an additional one, ending up with an extra appendage that makes them attractive to pet owners as a novelty. In metamorphosed individuals, however, the ability to regenerate is greatly diminished. The axolotl is therefore used as a model for the development of limbs in vertebrates"
betterexists
1 / 5 (1) Mar 27, 2014
Why NOT mess up DNA of Neotenic Axolotl larvae at their zygote level?
They can make 1000s of varieties of them....containing series of changes..from 1 or 2 changes to more & more!
Then, we can see when, why and how REGENERATION of it stops or gets enhanced.
Regeneration is THE MOST Important Field AFTER Ageing.
Not only an individual is losing parts of the body one is born with.....Society also is losing Most Accomplished Humans.
IT IS HIGHLY IMPERATIVE that both losses should be halted ASAP.
Once Energy is made easily available with Nuclear Fission or some Biofuel....The Planet OR our Solar System CAN tolerate the BURDEN of the Increased Populations!

I MEANT NUCLEAR FUSION!
betterexists
1 / 5 (1) Mar 27, 2014
Also Read this Blog "Regeneration: The axolotl story" dt: April 13, 2011 on blogs.scientificamerican "Sheer amount of damage that the axolotl can recover from is unbelievable. You can cut the spinal cord, crush it, remove a segment, and it will regenerate. You can cut the limbs at any level – the wrist, the elbow, the upper arm – and it will regenerate, and it's perfect. There is nothing missing, there's no scarring on the skin at the site of amputation, every tissue is replaced. They can regenerate the same limb 50, 60, 100 times. And every time: perfect. As if that isn't incredible enough, the axolotl is also over 1,000 times more resistant to cancer than mammals. But, there is only so much information one can get from observing the physiological changes that occur during limb amputation before you must look closer. The next step for Roy in his research on regeneration was taking a deeper look into the genetics of the animals by collaborating with German researchers to create the first transgenic, or genetically modified, axolotls."
Jaeherys
not rated yet Mar 27, 2014
Obokata's paper is impressive and not without merit. I have been doing similar but modified treatments and attaining promising results. There have been expression changes consistent with pluripotency and morphological/phenotypic changes characteristic of stem cells. Just because we have not been able to repeat these results doesn't mean they are not true. Everything about this process makes sense physiologically but since we have no idea of how it may actually work it's hard to know where other labs are going wrong, which is resulting in prevention of reprogramming.

This synthetic chromosome on the other hand is awesome and I cant wait for the day i can just send an order into sigma and have them deliver me a set of engineered human chromosomes. Oh what a day!
alfie_null
not rated yet Mar 28, 2014
Looking forward to the day when we can design our children. Or maybe not.
Returners
1 / 5 (2) Mar 28, 2014
Looking forward to the day when we can design our children. Or maybe not.


Not exactly.

I don't think we should be seeing engineered human chromosomes. Given human history it would potentially lead to some kind of "Applied Eugenics" based war...again...

However, I can see allowing couples who may be a carrier for a chromosomal defect to work around that by using all of their own DNA plus like a "good" version of the chromosome from a donor.
betterexists
1 / 5 (2) Mar 28, 2014
Looking forward to the day when we can design our children. Or maybe not.

Funny. You want to add a Prehensile Tail too?
I do not think it can support the human body weight on a Tree Branch...Branch will snap!
betterexists
1 / 5 (2) Mar 28, 2014
Looking forward to the day when we can design our children. Or maybe not.


Not exactly.

I don't think we should be seeing engineered human chromosomes. Given human history it would potentially lead to some kind of "Applied Eugenics" based war...again...

However, I can see allowing couples who may be a carrier for a chromosomal defect to work around that by using all of their own DNA plus like a "good" version of the chromosome from a donor.

You cannot stop water flowing downstream.
You have to take chances.
B Positive!
B Be Bee!
DistortedSignature
1 / 5 (1) Mar 28, 2014
...removing repeating sections of some 47,841 DNA base pairs, deemed unnecessary to chromosome reproduction and growth. Also removed was what is popularly termed junk DNA, including base pairs known not to encode for any particular proteins...


That part made me shudder, aren't we still discovering purposes for "junk DNA" all the time? I suppose this is on yeast so the consequences for slipping up are small, but it still makes me nervous about how much we don't know, since there are so many combinations and possibilities. We'll never know unless we try I suppose.
eric_in_chicago
1 / 5 (1) Mar 28, 2014
better,

my friend, you missed this article! very exciting!

http://phys.org/n...ies.html
betterexists
1 / 5 (1) Mar 28, 2014
Tinkering with Genes in the Genome! Removal/Replacement included. WoW!
More Importantly, Cancer Causing Genes of the Zygote should be BOTH Removed & Replaced starting with MICE and ending up with racing & farm animals....Eventually, obviously in Humans too either at Embryonic OR Adult Stages... A lot of Perfection of this Technique is hence needed!
betterexists
1 / 5 (1) Mar 28, 2014
...removing repeating sections of some 47,841 DNA base pairs, deemed unnecessary to chromosome reproduction and growth. Also removed was what is popularly termed junk DNA, including base pairs known not to encode for any particular proteins...


That part made me shudder, aren't we still discovering purposes for "junk DNA" all the time? I suppose this is on yeast so the consequences for slipping up are small, but it still makes me nervous about how much we don't know, since there are so many combinations and possibilities. We'll never know unless we try I suppose.

One can speak with forked tongue about science...Particularly regarding that of living organisms.....
We are BOTH Pretty much Advanced & Still AT INFANCY!
betterexists
1 / 5 (1) Mar 28, 2014
As Medical science too starts advancing...people start getting doubts...Why Tinkering with Chromosmes....Why This, Why That? Well, Researchers will have their Fun with Lab Animals first! Humans will be the fodder at the final round!
Now a days, many people around the world are sporting cellphones in their hands. Some around the world are living upto their 8o's and 90's even when lacking much medical attention or even without any medical attention at all like those damned Tortoises.
But it will be Extremely Foolish to say...Avoid Doctors in modern times....They are needed unfortunately at all ages, after all!
I am pretty sure Doctors particularly in the previous centuries did kill their patients due to their Outright Stupidity. In those days they might have lived longer without any intervention from their physicians.
One thing for sure...Band Aid Works!
Returners
1 / 5 (2) Mar 28, 2014
You cannot stop water flowing downstream.
You have to take chances.
B Positive!
B Be Bee!


Take a look at this article, and notice that they are removing all sequences currently deemed "junk" or "undesirable" including several of the more mobile genes associated with mutation.

First of all, the term "junk DNA" has already been proven to be a misnomer. The stuff does something, some time, some how, otherwise it probably wouldn't be there. Just because they can't figure out what it does in a laboratory doesn't mean it's "useless".

Extra copies of a gene are not necessarily "bad" because it provides a backup in case the original becomes damaged. This ought to be obvious, to anyone with an engineering oriented mind. I know why they removed it, due to the appearance of increased efficiency, but what is most efficient in the short term is not always best in the long term, else nobody would make redundant safety mechanisms, or back up computer files with that mindset.
Returners
1 / 5 (2) Mar 28, 2014
Viral DNA in the human genome might be useful as a long-term immune strategy.

A minimalist view like what has been taken with these yeasts, will potentially lead to the organism not having certain micro functions biologists just might not have discovered in the laboratory yet.

Think about it, materials scientists are constantly finding new properties of nanomaterials, but geneticists take the approach that if something doesn't have an obvious use they should just label it "junk" and remove it, when possible.

Hey, maybe that "junk" is there for "padding" to prevent two "useful" genes from merging via mutation.

Maybe it's parts of a hidden message from God.

I view it as "information". Maybe it is "useless" relative to genes, or maybe it has a chemical purpose unknown, or maybe "what it is" is not important, only it's presence, assuming a "padding" theory or a temporary micro-scaffold theory, like for cell division and such.
Returners
1 / 5 (2) Mar 28, 2014
This is akin to opening up an *.exe file in windows in binary and just deleting or zeroing anything you think you won't need in the next few days, and then saving the file again.

betterexists
1 / 5 (1) Mar 28, 2014
Chicken & Egg Affair. Which came first? Ill health OR Perfect Human.
We are provided with a Very Very Corrupt File;
It makes sense to INTERVENE After becoming ADEPT!
Are we Adept now? Nope.....For working with Yeast, Yeah! All The Best.
betterexists
1 / 5 (1) Mar 28, 2014
better,
my friend, you missed this article! very exciting!
http://phys.org/n...ies.html

zebrafish (Danio rerio) native to the Himalayan region & several others!
This mammal, The African spiny mouse obviously has advantages & disadvantages.
TheGhostofOtto1923
3 / 5 (2) Mar 28, 2014
I don't think we should be seeing engineered human chromosomes. Given human history it would potentially lead to some kind of "Applied Eugenics" based war...again...
What you religionists are really afraid of is the possibility that we will be able to fix the defects and diseases that your god seems incapable of fixing or unwilling to fix. Because humans you see are far more capable, and far less cruel and heartless, than your god has proven himself to be.
dtxx
not rated yet Mar 28, 2014
Re: Returners "junk dna" and "message from god"

I don't see any of the scientists claiming they know they will never need or have use for what they refer to here as junk dna. What they are claiming is that they removed some genes that fall into that class and the organism is still viable. How can we figure out what it does if we don't try these types of experiments.

Junk DNA being a message from god... wow, sure, of course it is in your fantasy addled mind. My toast got slightly burnt this morning and the sidewalk in front of my house has a new crack in it since that earthquake that recently hit L.A. Maybe those are messages from god too. Hey, look, I just took a shit and when I wiped the paper was totally clean. Must be a miracle from jesus trying telling me something! Take your god in the gaps bullshit and hit the road.
eag97a
not rated yet Mar 28, 2014
From an engineering perspective this breaktrough will push synthetic biology into practical applications soon enough. The real issue as discussed by the other commenters here is their reference to non-coding DNA as junk. These regions are imperfectly understood and may play a role in an organisms' evolutionary fitness and "evolvability". I fear that by having some limited success with designer organisms and genes scientists and biological engineers are heedless of the dangers of getting rid of these "junk" DNA and what role they play in evolution and if these designer organisms are released into the wild and all of the unintended consequences.

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