6 ms·

Scientists create ‘designer yeast’ in major step toward synthetic life

111 points by daegloe 10y ago

_rpd 10y ago
Here's the paper cited by the article ... http://science.sciencemag.org/content/355/6329/1040 http://science.sciencemag.org/content/355/6329/1040 Abstract: We describe complete design of a synthetic eukaryotic genome, Sc2.0, a highly modified Saccharomyces cerevisiae genome reduced in size by nearly 8%, with 1.1 megabases of the synthetic genome deleted, inserted, or altered. Sc2.0 chromosome design was implemented with BioStudio, an open-source framework developed for eukaryotic genome design, which coordinates design modifications from nucleotide to genome scales and enforces version control to systematically track edits. To achieve complete Sc2.0 genome synthesis, individual synthetic chromosomes built by Sc2.0 Consortium teams around the world will be consolidated into a single strain by “endoreduplication intercross.” Chemically synthesized genomes like Sc2.0 are fully customizable and allow experimentalists to ask otherwise intractable questions about chromosome structure, function, and evolution with a bottom-up design strategy.
- skosuri 10y ago
  Actually, it's 7 papers co-published in Science simultaneously. The others are: Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond: http://science.sciencemag.org/content/355/6329/eaaf4831 http://science.sciencemag.org/content/355/6329/eaaf4831 “Perfect” designer chromosome V and behavior of a ring derivative: http://science.sciencemag.org/content/355/6329/eaaf4704 http://science.sciencemag.org/content/355/6329/eaaf4704 Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome: http://science.sciencemag.org/content/355/6329/eaaf4791 http://science.sciencemag.org/content/355/6329/eaaf4791 Bug mapping and fitness testing of chemically synthesized chromosome X: http://science.sciencemag.org/content/355/6329/eaaf4706 http://science.sciencemag.org/content/355/6329/eaaf4706 Engineering the ribosomal DNA in a megabase synthetic chromosome: http://science.sciencemag.org/content/355/6329/eaaf3981 http://science.sciencemag.org/content/355/6329/eaaf3981 3D organization of synthetic and scrambled chromosomes: http://science.sciencemag.org/content/355/6329/eaaf4597 http://science.sciencemag.org/content/355/6329/eaaf4597 Along with an introduction: http://science.sciencemag.org/content/355/6329/1038 http://science.sciencemag.org/content/355/6329/1038 and perspective: http://science.sciencemag.org/content/355/6329/1024 http://science.sciencemag.org/content/355/6329/1024
  - sytelus 10y ago
    Are there any good resources to start in this field for non-biology majors? It seems they have now full end-to-end simulation so one can program yeast and even test it out at some extent with nothing but just a computer.
    - skosuri 10y ago
      They don't have that at all. This was a Herculean effort over 5 years with very few actual changes to the natural genome. I don't mean to make it seem not impressive (it is ambitious and impressive); it's that we are so far away from an end to end simulation of anything even orders of magnitude simpler than yeast.
    - 88e282102ae2e5b 10y ago
      Honestly, an introductory biology textbook is your best bet. But other response is correct: we can't even simulate a single protein well, much less an entire organism.
vikingcaffiene 10y ago
Do you want zombies? Because this is how you get zombies. ;-)
- q3r3qr3q 10y ago
  Or gholas.
- vikingcaffiene 10y ago
  Really with the downvotes??? Here let me try again in a more proper HN way: [collegiate voice] This is an exciting development and a massive step forward for the scientific community. However one must be careful to examine the ethical implications of such research as it can have unintended consequences. Creating new lifeforms without taking the time to fully understand the impact it would have on our fragile ecosystem could potentially be disastrous. [/end collegiate voice] In other words, we might make zombies. Geez downvoters, lighten up.
c0brac0bra 10y ago
But what does the beer it makes taste like?
- simtel20 10y ago
  Sadly they have started with bakers yeast so any beer will probably taste bad.
  - skadamou 10y ago
    "In the past, there were two types of beer yeast: ale yeast (the "top-fermenting" type, Saccharomyces cerevisiae) and lager yeast (the "bottom-fermenting" type, Saccharomyces uvarum, formerly known as Saccharomyces carlsbergensis). Today, as a result of recent reclassification of Saccharomyces species, both ale and lager yeast strains are considered to be members of S. cerevisiae. " https://www.beeradvocate.com/beer/101/yeast/ https://www.beeradvocate.com/beer/101/yeast/
dekhn 10y ago
Does the new genome contain overlapping genes? Natural Yeast have a number of overlapping genes. It would be really neat, since you can make synthetic chromosomes, to compare the effects of making genes overlap. This has implications (various RNA surveillance mechanisms can interfact with pairs of mRNAs that hybridize).
somebodynew 10y ago
With the pace of advancements in gene editing and the availability of biology maker-spaces, I expect that we're soon going to find out that the "3D printed guns" issue of hobbyist biology will be simple cells like yeast modified to synthesize illegal drugs. It may not be as efficient as industrial chemistry could be, but it only takes one entity producing such a cell before it will become a mainstay of illicit bathtubs everywhere. Every time I see an article like this I wonder why it hasn't already happened. We already have yeast that produce the active ingredients in cannabis, and I suspect the only reason nobody cares is because many people just grow plants anyway. How will this be handled once we can go a step further and make completely new genes that can make artificial drugs like LSD?
- ci5er 10y ago
  > and make completely new genes that can make artificial drugs like LSD? How do you mean? Lysergic acid is a naturally occurring biogenic substance.
  - nsxwolf 10y ago
    Lysergic acid diethylmide isn't.
- ceejayoz 10y ago
  Relevant: http://www.npr.org/sections/thesalt/2013/09/17/223345977/auto-brewery-syndrome-apparently-you-can-make-beer-in-your-gut http://www.npr.org/sections/thesalt/2013/09/17/223345977/aut... > The patient had an infection with Saccharomyces cerevisiae, Cordell says. So when he ate or drank a bunch of starch — a bagel, pasta or even a soda — the yeast fermented the sugars into ethanol, and he would get drunk. Essentially, he was brewing beer in his own gut. Cordell and McCarthy reported the case of "auto-brewery syndrome" a few months ago in the International Journal of Clinical Medicine.
  - dpatrick86 10y ago
    Getting infected with an illicit-chemical producing variant of that might be quite inconvenient!

111 points by daegloe 10y ago

_rpd 10y ago

Here's the paper cited by the article ... http://science.sciencemag.org/content/355/6329/1040 http://science.sciencemag.org/content/355/6329/1040 Abstract: We describe complete design of a synthetic eukaryotic genome, Sc2.0, a highly modified Saccharomyces cerevisiae genome reduced in size by nearly 8%, with 1.1 megabases of the synthetic genome deleted, inserted, or altered. Sc2.0 chromosome design was implemented with BioStudio, an open-source framework developed for eukaryotic genome design, which coordinates design modifications from nucleotide to genome scales and enforces version control to systematically track edits. To achieve complete Sc2.0 genome synthesis, individual synthetic chromosomes built by Sc2.0 Consortium teams around the world will be consolidated into a single strain by “endoreduplication intercross.” Chemically synthesized genomes like Sc2.0 are fully customizable and allow experimentalists to ask otherwise intractable questions about chromosome structure, function, and evolution with a bottom-up design strategy.

skosuri 10y ago
Actually, it's 7 papers co-published in Science simultaneously. The others are: Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond: http://science.sciencemag.org/content/355/6329/eaaf4831 http://science.sciencemag.org/content/355/6329/eaaf4831 “Perfect” designer chromosome V and behavior of a ring derivative: http://science.sciencemag.org/content/355/6329/eaaf4704 http://science.sciencemag.org/content/355/6329/eaaf4704 Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome: http://science.sciencemag.org/content/355/6329/eaaf4791 http://science.sciencemag.org/content/355/6329/eaaf4791 Bug mapping and fitness testing of chemically synthesized chromosome X: http://science.sciencemag.org/content/355/6329/eaaf4706 http://science.sciencemag.org/content/355/6329/eaaf4706 Engineering the ribosomal DNA in a megabase synthetic chromosome: http://science.sciencemag.org/content/355/6329/eaaf3981 http://science.sciencemag.org/content/355/6329/eaaf3981 3D organization of synthetic and scrambled chromosomes: http://science.sciencemag.org/content/355/6329/eaaf4597 http://science.sciencemag.org/content/355/6329/eaaf4597 Along with an introduction: http://science.sciencemag.org/content/355/6329/1038 http://science.sciencemag.org/content/355/6329/1038 and perspective: http://science.sciencemag.org/content/355/6329/1024 http://science.sciencemag.org/content/355/6329/1024
- sytelus 10y ago
  Are there any good resources to start in this field for non-biology majors? It seems they have now full end-to-end simulation so one can program yeast and even test it out at some extent with nothing but just a computer.
  - skosuri 10y ago
    They don't have that at all. This was a Herculean effort over 5 years with very few actual changes to the natural genome. I don't mean to make it seem not impressive (it is ambitious and impressive); it's that we are so far away from an end to end simulation of anything even orders of magnitude simpler than yeast.
  - 88e282102ae2e5b 10y ago
    Honestly, an introductory biology textbook is your best bet. But other response is correct: we can't even simulate a single protein well, much less an entire organism.

vikingcaffiene 10y ago

Do you want zombies? Because this is how you get zombies. ;-)

q3r3qr3q 10y ago
Or gholas.
vikingcaffiene 10y ago
Really with the downvotes??? Here let me try again in a more proper HN way: [collegiate voice] This is an exciting development and a massive step forward for the scientific community. However one must be careful to examine the ethical implications of such research as it can have unintended consequences. Creating new lifeforms without taking the time to fully understand the impact it would have on our fragile ecosystem could potentially be disastrous. [/end collegiate voice] In other words, we might make zombies. Geez downvoters, lighten up.

c0brac0bra 10y ago

But what does the beer it makes taste like?

simtel20 10y ago
Sadly they have started with bakers yeast so any beer will probably taste bad.
- skadamou 10y ago
  "In the past, there were two types of beer yeast: ale yeast (the "top-fermenting" type, Saccharomyces cerevisiae) and lager yeast (the "bottom-fermenting" type, Saccharomyces uvarum, formerly known as Saccharomyces carlsbergensis). Today, as a result of recent reclassification of Saccharomyces species, both ale and lager yeast strains are considered to be members of S. cerevisiae. " https://www.beeradvocate.com/beer/101/yeast/ https://www.beeradvocate.com/beer/101/yeast/

dekhn 10y ago

Does the new genome contain overlapping genes? Natural Yeast have a number of overlapping genes. It would be really neat, since you can make synthetic chromosomes, to compare the effects of making genes overlap. This has implications (various RNA surveillance mechanisms can interfact with pairs of mRNAs that hybridize).

somebodynew 10y ago

With the pace of advancements in gene editing and the availability of biology maker-spaces, I expect that we're soon going to find out that the "3D printed guns" issue of hobbyist biology will be simple cells like yeast modified to synthesize illegal drugs. It may not be as efficient as industrial chemistry could be, but it only takes one entity producing such a cell before it will become a mainstay of illicit bathtubs everywhere. Every time I see an article like this I wonder why it hasn't already happened. We already have yeast that produce the active ingredients in cannabis, and I suspect the only reason nobody cares is because many people just grow plants anyway. How will this be handled once we can go a step further and make completely new genes that can make artificial drugs like LSD?

ci5er 10y ago
> and make completely new genes that can make artificial drugs like LSD? How do you mean? Lysergic acid is a naturally occurring biogenic substance.
- nsxwolf 10y ago
  Lysergic acid diethylmide isn't.
ceejayoz 10y ago
Relevant: http://www.npr.org/sections/thesalt/2013/09/17/223345977/auto-brewery-syndrome-apparently-you-can-make-beer-in-your-gut http://www.npr.org/sections/thesalt/2013/09/17/223345977/aut... > The patient had an infection with Saccharomyces cerevisiae, Cordell says. So when he ate or drank a bunch of starch — a bagel, pasta or even a soda — the yeast fermented the sugars into ethanol, and he would get drunk. Essentially, he was brewing beer in his own gut. Cordell and McCarthy reported the case of "auto-brewery syndrome" a few months ago in the International Journal of Clinical Medicine.
- dpatrick86 10y ago
  Getting infected with an illicit-chemical producing variant of that might be quite inconvenient!