Current state of smallest genome aka minimal cell?
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Jonathan Cline
Apr 28, 2018, 1:47:29 PM4/28/18
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What is the current state of the art regarding the smallest viable genome? This was one of the most exciting areas of synbio. There are multiple angles to the problem. Some east coast bioinformatics labs were attempting to define the smallest genome via statistical methodologies. Southern california labs were trying to evolve lines into ever smaller genomes. Some synthesis labs were trying to synthesize the minimal cell. Microfluidics biochem labs were trying to synthetically spawn life from organic chemistry. It is a landmark goal which defines the smallest packet of bioinformation required for life. Would someone summarize the status as of 2018?
Koeng
Apr 29, 2018, 12:38:32 AM4/29/18
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Howdy,
TL;DR: understanding a Cell is still underway. Scientists are aiming to build bottom up rather than top down. JCVI is working on minimal eukaryotic cell. Look up “Build-a-Cell” to find an out of date website.
I think I’m in a pretty good position to answer this. Drew Endy’s Lab (which I work at) is current running a project called “build-a-cell”, which basically is a project to understand a cell (different than smallest). If ya take a look at JCVI’s Mycoplasma, there’s like ~120 completely unknown genes. What do they do? Why are they essential? The theory I’ve heard from the folks at JCVI is that many of these are transporters for different molecules. Because they’re membrane bound, they’re more difficult to understand as a system than their biosynthetic counterparts in larger cells. Basically: if we want to learn how to build a cell, mycoplasmas probably aren’t the way to go. They can’t even live on minimally defined media!
I know there’s a similar project underway in Europe for building a cell, headed by some very smart scientists. They seem much more concerned by the biomechanics and such of these systems than a complete engineering approach (asking perhaps “how does this system work” on a scientific level instead of “what does this system do and how do I use it”). They’re still great engineers, don’t get me wrong, but what we are doing is slightly different.
The west coast build-a-cell collective is leaning towards Cell Free systems right now as a way to understand how a cell works by trying to build a cell from the ground up. I think this approach is the most promising.
On a personal note, I presented at one of the BioHTPs on my idea of what a buildable genome was. In essence, what I believed and still believe is that a much larger community needs to be involved in this exploration. Akin to the Linux bazaar rather than a windows cathedral. An open source community of biologists working towards a goal independently but collaborating in a waythat is collectively useful and scalable. The simple fact that many people don’t know about the Bi-annual buildacell meetings is a testament to the current scalability. Heck, JCVI isn’t even really working on Mycoplasma anymore (by who knew that other than the inside parties, right?)
Soooo right now at the BioBricks FreeGenes Project (I help lead that effort, having marketed it much yet because I’m still scaling our robots, submission->shipping, etc) we are synthesizing every single gene from Mycoplasma JCVI syn3.0, genitalium, and pneumoniae, plus all the genes from Mesoplasma florum (also the essential gene sets from Bacillus subtilis and E. coli) all codon optimized for E. coli expression (MoClo compatible). We already have the gene cloning down, so it should take us about 2 weeks to clone those 3mbps, but in the future the aim is to get protein purification automated with the opentrons so we can begin discovering all the functions and combinations of all those genes. If you want any, shoot me an email.
Anyway, enough rant. If you have any questions about what’s going on, feel free to respond to this. Cheers,
Koeng
TL;DR: understanding a Cell is still underway. Scientists are aiming to build bottom up rather than top down. JCVI is working on minimal eukaryotic cell. Look up “Build-a-Cell” to find an out of date website.
I think I’m in a pretty good position to answer this. Drew Endy’s Lab (which I work at) is current running a project called “build-a-cell”, which basically is a project to understand a cell (different than smallest). If ya take a look at JCVI’s Mycoplasma, there’s like ~120 completely unknown genes. What do they do? Why are they essential? The theory I’ve heard from the folks at JCVI is that many of these are transporters for different molecules. Because they’re membrane bound, they’re more difficult to understand as a system than their biosynthetic counterparts in larger cells. Basically: if we want to learn how to build a cell, mycoplasmas probably aren’t the way to go. They can’t even live on minimally defined media!
I know there’s a similar project underway in Europe for building a cell, headed by some very smart scientists. They seem much more concerned by the biomechanics and such of these systems than a complete engineering approach (asking perhaps “how does this system work” on a scientific level instead of “what does this system do and how do I use it”). They’re still great engineers, don’t get me wrong, but what we are doing is slightly different.
The west coast build-a-cell collective is leaning towards Cell Free systems right now as a way to understand how a cell works by trying to build a cell from the ground up. I think this approach is the most promising.
On a personal note, I presented at one of the BioHTPs on my idea of what a buildable genome was. In essence, what I believed and still believe is that a much larger community needs to be involved in this exploration. Akin to the Linux bazaar rather than a windows cathedral. An open source community of biologists working towards a goal independently but collaborating in a waythat is collectively useful and scalable. The simple fact that many people don’t know about the Bi-annual buildacell meetings is a testament to the current scalability. Heck, JCVI isn’t even really working on Mycoplasma anymore (by who knew that other than the inside parties, right?)
Soooo right now at the BioBricks FreeGenes Project (I help lead that effort, having marketed it much yet because I’m still scaling our robots, submission->shipping, etc) we are synthesizing every single gene from Mycoplasma JCVI syn3.0, genitalium, and pneumoniae, plus all the genes from Mesoplasma florum (also the essential gene sets from Bacillus subtilis and E. coli) all codon optimized for E. coli expression (MoClo compatible). We already have the gene cloning down, so it should take us about 2 weeks to clone those 3mbps, but in the future the aim is to get protein purification automated with the opentrons so we can begin discovering all the functions and combinations of all those genes. If you want any, shoot me an email.
Anyway, enough rant. If you have any questions about what’s going on, feel free to respond to this. Cheers,
Koeng
John Griessen
Apr 29, 2018, 1:41:13 PM4/29/18
to diy...@googlegroups.com
On 04/28/2018 11:38 PM, Koeng wrote:
> Soooo right now at the BioBricks FreeGenes Project (I help lead that effort, having marketed it much yet because I’m still scaling our robots, submission->shipping, etc) we are synthesizing every single gene from Mycoplasma JCVI syn3.0, genitalium, and pneumoniae, plus all the genes from Mesoplasma florum (also the essential gene sets from Bacillus subtilis and E. coli) all codon optimized for E. coli expression (MoClo compatible). We already have the gene cloning down, so it should take us about 2 weeks to clone those 3mbps, but in the future the aim is to get protein purification automated with the opentrons so we can begin discovering all the functions and combinations of all those genes.
Please tell us more about protein purification with the opentrons.
> Soooo right now at the BioBricks FreeGenes Project (I help lead that effort, having marketed it much yet because I’m still scaling our robots, submission->shipping, etc) we are synthesizing every single gene from Mycoplasma JCVI syn3.0, genitalium, and pneumoniae, plus all the genes from Mesoplasma florum (also the essential gene sets from Bacillus subtilis and E. coli) all codon optimized for E. coli expression (MoClo compatible). We already have the gene cloning down, so it should take us about 2 weeks to clone those 3mbps, but in the future the aim is to get protein purification automated with the opentrons so we can begin discovering all the functions and combinations of all those genes.
Koeng
Apr 30, 2018, 6:42:04 PM4/30/18
to DIYbio
Sure.
The OpenTrons can do protein purification using magbeads with their magdeck. Currently for the OT, I believe there is some work on having the magnets next to the pipette tips, so you can wash the material in the tip and get a much higher protein purification yield. Protein purification with a magdeck is great for getting a lot of small things (96 well purification is totally possible), but per yield protein, it's about 100x less cost effective than column based. What makes sense is first purifying protein with a magdeck on the opentrons to quickly test the protein, and once you are happy with the results, move it to a larger purification system that uses columns.
OpenTrons can also do columns if you're a wizard and hack the OT1 properly, but since that version is getting less and less support, I think OT2 is the way to go for small-volume purification, and then subsequently scaling up with an idiosyncratic pump-system.
It'd be great if there was a nice high-throughput protein purification machine, but I don't think there is.
The other option is getting the bead prices down to match columns, but good luck with that.
Koeng
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