National Science Foundation Funds Synthetic Cell Development

Vincent Noireaux - crop
VINCENT NOIREAUX

Not to be outdone by Dutch, German and other Europeans now officially dabbling in synthetic cell research, America’s National Science Foundation has thrown its hat into the ring on funding synthetic cell development, per its April 18, 2018 letter to colleagues inviting proposals on the design and engineering of synthetic cells and cell components ($100K for relevant conferences, $300K re multicomponent subsystems, and up to $1M for research on the “pseudo-cell”). In May, following its call for proposals, NSF co-sponsored a synthetic and artificial cells roadmap meeting in Alexandria, Virginia with a handful of scientists already working in the field presenting and others in the audience looking to be educated.

Videos of the presentations are posted online and are well worth viewing.

One of the most substantive presentations was by Vincent Noireaux, a University of Minnesota physicist, whose lab I visited in 2014.  Noireaux, a former protégé of Rockefeller University’s Albert Libchaber, has been funded by DARPA (Defense Advanced Research Projects Agency) in recent years for his work on the minimal cell.

Libchaber told me at a 2014 meeting in his Rockefeller University office: “Vincent thinks he will have a minimal cell that can self-replicate within five years.”

My interviews with both Vincent Noireaux and Albert Libchaber are featured in The Origin of Life Circus: A How To Make Life Extravaganza.  Excerpts from the Noireaux interview follow my wrapup of the NSF gathering in Alexandria.

OriginOfLife(Front)_02_06_16.jpg

Another key presenter at the NSF meeting was Clyde Hutchison, a biochemist and microbiologist known for his role in creating “Synthia” eight years ago at J. Craig Venter Institute

Clyde Hutchison
CLYDE HUTCHISON

Hutchison reminded the audience that JCVI had already made a synthetic cell, further advising that he realized that claim irritates people.  Hutchison then described what JCVI means by a synthetic cell: 

“We have built a synthetic DNA genome and installed it in the cytoplasm of a living cell.  This produces a cell controlled by the synthetic genome.”

Hutchison added:

“Someday it will be possible to assemble a cell from non-living components (ribosomes, tRNAs, enzymes, membranes, etc.) but this seems very difficult at present.”

He said the long-term goal is an atom model of the synthetic cell.  Hutchison also announced that JCVI was collaborating on further development of the cell with Zan Luthey-Schulten’s lab at the University of Illinois, Urbana-Champaign.  Luthey-Schulten was one of the organizers of the NSF Alexandria workshop.

Eberhard Bodenschatz, a physicist and director of Max Planck Institute for Dynamics and Self-Organization in Gottingen, Germany gave the European perspective on synthetic cells.  Bodenschatz said that the Max Planck Society (Max Planck Gesellschaft, a  German non-profit association with a budget of €2B) is establishing a new institute on origins of life, and that five of the MPG schools will be offering MS and PhD degrees in the Matter to Life field beginning 2019. 

Eberhard Bodenschatz
EBERHARD BODENSCHATZ

Bodenschatz is hopeful that the Max Planck program on synthetic cell development, known as MaxSynBio, will be funded in 2020 at €25M through the following sources:

(1)  “Biotechnologie 2020+” through BMBF (Federal Ministry for Education and Research)

(2)   Max Planck Society (MPG)

(3)   Core budgets of participating Max Planck Institutes (MPI)

He also emphasized that a dialogue with the public on synthetic cell development is critical and that Peter Dabrock, a theologian who sits on the Ethics Council of the German government, will oversee “challenges at the interface of science and society.”  

Bodenschatz defined a living system as “a nonlinear, open system with chemical diversity driven far from equilibrium that consumes energy and generates structure showing emergent collective behavior.”  He considers the cell a technical system.

Bodenschatz said that there was as yet no genome in the MaxSynBio approach to synthetic cell development, that scientists there wanted to see how far into development self-organization would take them.  He added that the Dutch and Max Planck synthetic cell initiatives are very similar, except that the Dutch have now added the genome to their scheme.

[See my interview with Bert Poolman, posted at HuffPost, for more on the €19M Dutch synthetic cell program BaSyC.]

It is unclear how much China is spending on synthetic cell development, but surely Tetsuya Yomo’s PI status at East China Normal University’s Institute of Biology and Information Science means China is seriously investigating.  Also, Bodenschatz in his presentation referred to his participation at a Shanghai workshop that preceded both the German and Dutch initiatives, the NSF Alexandria workshop, and last summer’s Ringberg Castle symposium in Bavaria on building a synthetic cell—the latter featuring:  Jack Szostak (“Why make synthetic cells?”), Bert Poolman, John Sutherland, Eberhard Bodenschatz, Drew Endy, Sheref Mansy, and Mary Voytek, among others.

There was some banter at the recent NSF gathering about the difference between a synthetic cell and an  artificial cell with nothing resolved. . .

Vincent Noireaux’s NSF talk on cell free expression laid out the basics on cell parts:  information, compartment, metabolism—saying all three have to be successfully linked to make a synthetic cell.  He listed various bottom-up synthetic cell systems scientists refer to and gave his take on a few of the systems:

(1) protocell/coacervate—origin of unicellular life, peptide, RNA, fatty acids

(2) artificial cell—cell-sized self-sustaining homeostatic compartment made of natural and artificial molescules

(3) minimal cell—synthesis of a self-reproducing cell-sized compartment, natural molecular machinery (transcription, translation, phospholipids).

Noireaux next focused on the technical aspects of creating a minimal cell and said the objectives were (a) recapitulation of some cellular functions, and (b) self-replication of a cell-sized compartment (200-400 genes required).

He also described various challenges in the information, self-assembly, and metabolism blocks.  Noireaux termed self-organization a “poorly characterized process” and said we need more attention to cytoskeleton development. He also noted that understanding how to make liposomes with complex phospholipid mixtures is still very limited.  And that gene regulation needs work, among other challenges.

Richard M. Murray, a Caltech professor of bioengineering, followed up with a five-systems breakdown in building a synthetic cell: 

(1) spatial organization – cell wall and internal structure

(2) metabolic subsystem – power supply, important chemicals

(3) sensing & signaling – sense the local environment and communicate with other cells

(4) regulation & computation – maintain the internal state and control interactions, motion

(5) actuation – move in/affect environment (physical and chemical).

Richard Murray
RICHARD M. MURRAY

As an engineer Murray thinks replication is not so important in building a synthetic cell. Murray said it will be 30 years before the synthetic cell is developed and that no single lab can do it—it has to be a collaborative effort.

Noireaux made brief mention of a collaboration with Murray.

Drew Endy, a Stanford University bioengineer who Esquire magazine named one of the 75 most important people of the 21st century (along with Tiger Woods, Michael Milken, Arnold Schwarzenegger, Bill & Hillary Clinton et al.), and who participated in the Ringberg Castle syncell symposium in Bavaria, cautioned about leaving out the cultural aspect to making a synthetic cell.

Drew Endy
DREW ENDY

Endy considers the job 80% technical and 20% “anthropological”.  He said making the cell would not be acheived just within academic circles. Endy also addressed motive in syncell development asking:  “Are we simply going to invoke a name of building cells to do what we’re already doing?”

Drew Endy cartoon

One scientist in the audience from the Marvel comics camp cheered on the notion of a synthetic cell escaping outside its environment. . .

Vincent Noireaux in final thoughts about the NSF Alexandria meeting voiced his confidence that there was already a lot in place on synthetic cell development.  Indeed, one or two scientists in the room seemed bewildered by the briefing.

My chat with Vincent Noireaux on “How to Make a Minimal Cell”: 

Vincent Noireaux 27.jpg.jpg

May 12, 2014

“It was positively springtime in Minneapolis. Raining lightly, glistening, a bit windy. Following my non-direct flight from New York, the air was like a rush of Peter’s Blend (a serious Bleecker Street roast).

I was excited by Vincent Noireaux’s invitation to visit his lab at the University of Minnesota, his minimal cell lab. Noireaux  offered to meet me at the airport.  But since I’d never been to Minneapolis, I decided to make my own way into town, to explore.

Vincent Noireaux is 40ish, quick, with attractive blue eyes and an unmistakably-French smile. His PhD is in physics from France’s Institut Curie.

As a postdoc, Noireaux collaborated with Albert Libchaber on a synthetic cell system, working in Libchaber’s condensed matter physics lab at Rockefeller University.  Libchaber is formerly a director of research at CNRS (French National Center for Scientific Research). 

We met in Noireaux’s office. In the grass outside his building are a pair of condensed matter sculptures Noireaux introduced me to, recent additions to the university landscape called Spannungsfeld, meaning “tension field.”

The pieces are the creation of German quantum physicist-turned-artist Julian Voss-Andreae, now an Oregonian (or “Orygunian,” as they say).  The 10-foot tall male and female torsos each weigh 1.5 tons and are made of sliced steel and open space. Viewed from various perspectives, the figures appear to change form, from solid to hologram.

Voss-Andreae says the sculptures are “a metaphor for the counterintuitive world of quantum physics.”

Inside Vincent Noireaux’s office I notice a baby carriage.  Noireaux informs me that his wife is a scientist as well.  She’s now finishing her PhD in physics at the University of Minnesota.

Over a Starbuck’s coffee, Noireaux tells me he grew up in the French countryside.  His father is a government official and his mother a banker. 

On the day of my visit, Noireaux was in the middle of a move to the university’s 3M building, to a spacious new lab, which I toured — featuring state-of-the-art equipment and windows looking out into the Minnesota sky. It’s a minimal cell research facility largely funded by DARPA (Defense Advanced Research Projects Agency).

But first we took a spin through Noireaux’s old cramped and windowless E. coli lab, the door posted BIOHAZARD.

biohazards - 2

Test tubes filled with fascinating liquid were being readied for transport.  Noireaux noticed that a floor freezer was a bit ajar, and he quickly put a make-shift weight on top of the lid to close it.  We next passed an innocent-looking white refrigerator that Noireaux opened to reveal shelves of tubes of much less innocent-looking stuff.  We then proceeded out of the lab.

I didn’t want to spend more time than necessary around the tubes, frankly, considering the biohazard sign.  But I did wonder what DARPA’s interest was in Noireaux’s minimal cell project. 

Noireaux says even he doesn’t know what he might discover with his minimal cell research.

Noireaux works with a team of graduate students and one postdoc, Filippo Caschera, who he introduced to me in the room adjacent to the old lab. Caschera was busily organizing the move. He’d been a researcher in Venice, Italy at Norm Packard’s company ProtoLife before coming to work with Noireaux and at Pier Luigi Luisi’s minimal cell lab in Rome.

During our interview Noireaux described his current work on the minimal cell and also mapped out who some of the other synthetic cell players are.

Suzan Mazur:  Can we walk through the three types of synthetic cells?  And would you tell me at what stage of development you are with your system?

Vincent Noireaux:  I am now finishing a review with my postdoc associates in the lab. What we see are the following three approaches to making a synthetic cell.

First is the protocell, which is about origin of life. It involves creating a self-reproducing unicellular entity with the basic molecules of life, including molecules for the membrane, ions, some genetic information like RNA. 

The second approach is the minimal cell.  The minimal cell is made of natural molecules and components. It’s more sophisticated.  Machineries such as transcription and translation are used to execute the DNA programs, to try to create a self-reproducing unicellular system. It’s known now that approximately 200 – 400 genes are necessary to make a minimal cell that would be able to reproduce itself.

The third approach is the artificial cell. I define artificial cell as a synthetic cell system that incorporates non-natural molecules and components. I can give the example of block copolymers, which look like phospholipids and self-assemble into membranes.  Eventually it is thought artificial cells can be made from them.

In my laboratory here at the University of Minnesota, we’re working on minimal cells. We have developed a cell-free transcription-translation system to execute large DNA programs in vitro.

Suzan Mazur:  Cell-free.

Vincent Noireaux:  It’s in vitro. There’s just no cell there.  We extract the molecular machineries (for transcription and translation) to express DNA programs. We developed recently what we call the cell-free transcription-translation toolbox, which allows us to express relatively complicated DNA programs.

The largest one we’ve executed so far is a natural DNA program.  We just did a demonstration to challenge the system with the genome of a virus, a virus from bacteria — bacteriophage.  This system is approximately 60 genes. It’s still not the 200 to 400 genes needed for a minimal cell, but we demonstrated that the system we developed can take or execute very large DNA programs.

This electron microscope image is a picture of the system.  You can see the phages that are made after a few hours entirely synthesized from the genome of these viruses. So we really have a system now. It’s a liquid solution, where you put some DNA in it and the DNA is expressed. We are able now to make very well defined living entities, even though it’s a virus and needs a host.  It’s a complex, self-assembled information-based system.

Suzan Mazur:  Do you consider a virus living?

Vincent Noireaux:  It’s a very good question.  It does require a host.  It reproduces through a host. So whether it’s living or not is a little bit debatable.

We have developed this system, which we call a cell-free transcription-translation platform, that allows us to execute DNA programs in vitro.  We are returning now to the minimal cell.  We want to encapsulate the system into liposomes and execute DNA programs that encode for essential functions of living cells.

What we do is take free cells and extract the complex machinery to express DNA. We remove everything, all of the genetic information of the cells, and we have all of these molecules we then use to express DNA that we synthesize in the laboratory.  We can encapsulate that into liposomes.

Suzan Mazur:  In trying to get it to self-reproduce, how close do you think you are? And what is the problem at this point in getting it to self-reproduce?

Vincent Noireaux:  That’s a very good question. The problem is. The cell is made of three parts [draws diagram]: information, metabolism, and there is self-organization. Each of these parts is made of molecular machineries, each of these parts is essential to make a cell.

The problem we have is to understand how these parts talk together.  The real problem is the integration of these three parts in a compartment.  Information is the DNA program, its genetic composition and its regulation. Metabolism is energy or the nutrients, at least at the beginning. And self-organization occurs with expression of proteins, which are able to make very specific assemblies and structures in specific locations.  It is a real problem integrating these three parts in a container and coordinating their actions.

I have been working a lot on information and a system to express DNA.  In the past few years, this has developed nearly to a system.    

We’ve also worked to develop a system that can express protein for a very long time based on energy. Our platform is now more robust energetically.

Finally there is self-organization. We’re trying to understand how when some proteins are expressed together, it is possible to make very specific structures.

In a sort of test before the minimal cell, we are looking at phages.  In a certain amount of time, minutes or hours, you get something that is incredibly well defined.  There are many things related to cells that we understand with this system, which recapitulate all of the fundamental steps of genetic information and its expression.

So you have information, you express a bunch of molecules, and they create something perfectly well defined.  The phage in this case is a crystal, it’s a crystal with DNA inside it.

The ultimate goal of what we are doing is the minimal cell, but first we have to understand the relationship between information and self-organization.  Where we are right now is that we have the most versatile and powerful cell-free transcription-translation system reported so far for synthetic biology applications.

Suzan Mazur: So time-wise where are you with development of a minimal cell that can self-reproduce? 

Vincent Noireaux:  It may be early to give an estimation of how many years.  We have a system which we think is relatively close to a minimal cell.

Suzan Mazur:  How does recent creation of an organism with an expanded genetic code intended for use in the drug industry affect your current research, if at all?

Vincent Noireaux:  For now, this work is relatively far from what we do.  The current concern for us is to develop genetic regulation that will coordinate the expression of the genes.  How to make a synthetic genome that works.  

Suzan Mazur:  Your interest is also in the minimal cell for use in drug delivery, I understand.  In light of current thinking about top-down evolution, that evolution happens top down — tissues, organs, cells — and systemically,  that it is not gene-centered — how do you think that plays out regarding human exposure to these future drugs.

Vincent Noireaux:  If we get a minimal cell, we can engineer it for specific application such as drug delivery or use it as a factory to synthesize new drugs.  First, what is the state of the art right now in building a minimal synthetic genome?  It is still difficult to make genetic circuits of a few tens of genes with predictable behavior.  So we are relatively far, in that sense, from the minimal cell of 200-400 genes. 

Does this work have ethical problems.  Is it dangerous?

Suzan Mazur:  Yes, that’s my question.  Is it dangerous if it’s used to produce drugs people are taking?

Vincent Noireaux: I think we are relatively far from such achievements.  The synthesis of a real minimal cell that can self-reproduce presents more potential ethical problems than the applications that would come after.

Suzan Mazur:  Could drugs made via the minimal cell using natural DNA prove more problematic once in the bloodstream than, say, a vaccine made using synthetic nucleotides?

Vincent Noireaux:  Here I do not have the elements to answer this question.

Suzan Mazur:  But if the minimal cell is used to produce drugs that people are taking–

Vincent Noireaux:  Yes. You can think about that.  Synthetic DNA really depends on what you do with it and where you express it. 

My work is more about natural DNA in a container for the minimal cell.  The first minimal cells able to reproduce themselves will still be relatively fragile mechanically.  They’re not going to have the real robustness of a cell as we know it.  They’re not going to be dangerous, in the sense that they will certainly not be competitive. 

Suzan Mazur:  What I’m referring to is the epigenetic factor — evolution that’s top-down and systemic — organs, cells, tissues — not gene-centered. What could happen with the introduction into the human bloodstream of these drugs?

Vincent Noireaux:  Your point is good definitely.  If we have a minimal cell, how quickly is it evolvable?  How quickly can it diverge and become something very robust?  That is completely unclear what can happen. 

Suzan Mazur:  It’s down the road and would have to go through all kinds of trials.

Vincent Noireaux:  Exactly. Trials and engineering after that.  Absolutely.

Suzan Mazur: Who would you say the key protocell, minimal cell, artificial cell players are?

Vincent Noireaux: Protocell, I would say Jack Szostak at Harvard.  Pier Luigi Luisi and all the family of Luisi, Pasquale Stano et al. at the University of Rome3 — they do both protocell and minimal cell.

[Note: Pier Lusi Luisi advises the Luisi lab is winding down due to lack of funding.]

Vincent Noireaux:  There’s the group of Steen Rasmussen at the University of Southern Denmark.  They do modeling and both protocell and minimal cell. 

Suzan Mazur: I interviewed both Rasmussen and Luisi.  I haven’t interviewed the Japanese researchers, like Tetsuya Yomo at Osaka who’s working on the minimal cell.  Albert Libchaber mentioned a former student of his, Yusuke Maeda now at Kyoto University, also working on minimal cell and protocell.  I saw Maeda’s Princeton Origins presentation last year.

Vincent Noireaux:  There is also Takuya Ueda at the University of Tokyo.  Ueda does minimal cell systems.  There’s Sheref Mansy of the University of Trento in Italy, as well as Christophe Danelon in The Netherlands at Delft University of Technology.

Suzan Mazur: One of your associates here was formerly a researcher at Norman Packard’s ProtoLife lab, wasn’t he?

Vincent Noireaux:  Absolutely. Filippo Caschera. He was a postdoc at ProtoLife and got his PhD at the University of Southern Denmark. He was working with Steen Rasmussen and others.

Also, there’s Pierre-Alain Monnard at the University of Southern Denmark.

The third synthetic cell is the artificial cell. The artificial cell is when you have synthetic components. More soft-matter people.  Daniel Hammer at University of Pennsylvania is one scientist working on the artificial cell.

Suzan Mazur: There is also the Simons Foundation and its research team on origins of life.  Actually, I think Sheref Mansy is part of that collaboration.

Vincent Noireaux:  Our work here on the minimal cell is related to the origin of life but on a slightly more sophisticated level where we really try to understand the minimum genetic system.  It’s also a question of physics, how physically to make a self-reproducing entity.

Suzan Mazur:  Research on origin of life is being increasingly privately funded meaning the research can be done more quietly.  However, less public scrutiny may be a problem when the research is origin of life/protocell development.

Vincent Noireaux:  I don’t think there is a danger here, major results would be published.  It is nice and essential that foundations support basic science.”

 

 

 

 

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