Scientists create ‘designer yeast’ in major step toward synthetic life | Hacker News Reader

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

washingtonpost.com

111 pointsdaegloe23 comments

Here's the paper cited by the article ...

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.

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

“Perfect” designer chromosome V and behavior of a ring derivative: 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

Bug mapping and fitness testing of chemically synthesized chromosome X: 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

3D organization of synthetic and scrambled chromosomes: http://science.sciencemag.org/content/355/6329/eaaf4597

Along with an introduction: http://science.sciencemag.org/content/355/6329/1038

and perspective: http://science.sciencemag.org/content/355/6329/1024

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.

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.

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.

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?

> and make completely new genes that can make artificial drugs like LSD?

How do you mean? Lysergic acid is a naturally occurring biogenic substance.

Lysergic acid diethylmide isn't.

Relevant: 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.

Getting infected with an illicit-chemical producing variant of that might be quite inconvenient!

Just being infected with that, and being pulled over with a high BAC would be too. Clever way to get someone out of the way too, without killing them. Who would believe a drunk driver vs. their blood test results and a video of them obviously intoxicated?

You worry about that. I'll worry about someone growing a fungus or microbe strain to wipe out crops, livestock, or people.

Already exists:

https://www.theguardian.com/science/2015/aug/13/yeast-cells-...

The pathway for cocaine synthesis is known. https://www.ncbi.nlm.nih.gov/nuccore/KC140149 and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4281001/ I'd be surprised if drug cartels with all their money hadn't tried to modify plants or yeast to reduce their risks.

When you mentioned "3D printed guns", it brought to mind the yeast strain in the novel "Rule 34" modified to synthesize spider silk for use in garden shed weapon factories. :)

> Every time I see an article like this I wonder why it hasn't already happened

Evolution, unfortunately, ruins all the fun. Producing all those proteins to make your drug of choice puts a large burden on the cells - any of them that lose those genes to mutations in the DNA will be able to grow slightly faster and eventually take over the entire culture.

But what does the beer it makes taste like?

Sadly they have started with bakers yeast so any beer will probably taste bad.

"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/

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).

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

Or gholas.

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.

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