Synthetic biology is one of the most exciting strategies for the investigation of living organisms and lies at the intersection of biology and engineering. Originally developed in prokaryotes, the idea of deciphering biological phenomena through building artificial genetic circuits and studying their behaviors has rapidly demonstrated its potential in a broad range of fields in the life sciences. From the assembly of synthetic genomes to the generation of novel biological functions, yeast cells have imposed themselves as the most powerful eukaryotic model for this approach. However, we are only beginning to explore the possibilities of synthetic biology, and the perspectives it offers in a genetically amenable system such as yeast are endless.
Highlights • Synthetic biology creates cell-based solutions for important biomedical problems. • Applications range from drug discovery and molecular diagnostics to cell-therapies. Synthetic biology applies engineering principles to biological systems and reprograms living cells to perform novel and improved functions. In this review, we first provide an update of common tools and design principles that enable user-defined control of mammalian cell activities with spatiotemporal precision. Next, we demonstrate some examples of how engineered mammalian cells can be developed towards biomedical solutions in the context of real-world problems.
To obtain an alternative source for the production of gentiopicroside, here genomic DNA segments of the medicinal plant Gentiana macrophylla were randomly transferred into Hansenula polymorpha by 25 KeV nitrogen ions (N+) at a dose of 2.5 × 1016 ions/cm2 under vacuum pressure of 1 × 10−3 Pa. To screen for potential gentiopicroside-producing recombinant yeast strains, geraniol 10-hydroxylase (G10H) and secologanin synthase (SLS) involved in the gentiopicroside biosynthesis pathway were used as molecular markers. Based on the conserved protein sequences of G10H and SLS, degenerate primers were designed and used for colony polymerase chain reaction (PCR). PCR-positive results for both the G10H and SLS genes were obtained in 79 out of 653 transformants by low-energy ion beam-mediated transformation. These 79 potential gentiopicroside-producing strains were further analysed by Fehling's test, thin-layer chromatography, high performance liquid chromatography and high performance liquid chromatography-mass spectrometry. The results showed that the retention time and ion peaks of the sample from one stable recombinant strain designated as DL67 were consistent with those of the gentiopicroside standard. The corresponding gentiopicroside yield was 8.41 mg/g dry cell weight after strain DL67 was cultured for 96 h. This could offer a new starting point for the construction of recombinant yeasts for production of medicinal plant compounds.
We report a toolbox for exploring the modular tuning of genetic circuits, which has been specifically optimized for widespread deployment in STEM environments through a combination of bacterial strain engineering and distributable hardware development. The transfer functions of sixteen genetic switches, programmed to express a GFP reporter under the regulation of the (acyl-homoserine lactone) AHL-sensitive luxR transcriptional activator, can be parametrically tuned by adjusting high/low degrees of transcriptional, translational, and post-translational processing. Strains were optimized to facilitate daily large-scale preparation and reliable performance at room temperature in order to eliminate the need for temperature controlled apparatuses, which are both cost-limiting and space-constraining. The custom-designed, automated, and web-enabled fluorescence documentation system allows time-lapse imaging of AHL-induced GFP expression on bacterial plates with real-time remote data access, thereby requiring trainees to only be present for experimental setup. When coupled with mathematical models in agreement with empirical data, this toolbox expands the scalability and scope of reliable synthetic biology experiments for STEM training.
Over the last decade, functionally designed DNA nanostructures applied to lipid membranes prompted important achievements in the fields of biophysics and synthetic biology. Taking advantage of the universal rules for self-assembly of complementary oligonucleotides, DNA has proven to be an extremely versatile biocompatible building material on the nanoscale. The possibility to chemically integrate functional groups into oligonucleotides, most notably with lipophilic anchors, enabled a widespread usage of DNA as a viable alternative to proteins with respect to functional activity on membranes. As described throughout this review, hybrid DNA-lipid nanostructures can mediate events such as vesicle docking and fusion, or selective partitioning of molecules into phase-separated membranes. Moreover, the major benefit of DNA structural constructs, such as DNA tiles and DNA origami, is the reproducibility and simplicity of their design. DNA nanotechnology can produce functional structures with subnanometer precision and allow for a tight control over their biochemical functionality, e.g., interaction partners. DNA-based membrane nanopores and origami structures able to assemble into two-dimensional networks on top of lipid bilayers are recent examples of the manifold of complex devices that can be achieved. In this review, we will shortly present some of the potentially most relevant avenues and accomplishments of membrane-anchored DNA nanostructures for investigating, engineering, and mimicking lipid membrane-related biophysical processes.
This week, scientists will gather in Washington, D.C., for an annual meeting devoted to gene therapy—a long-struggling field that has clawed its way back to respectability with a string of promising results in small clinical trials. Now, many believe the powerful new gene-editing technology known as CRISPR will add to gene therapy’s newfound momentum. But is CRISPR really ready for prime time? Science explores the promise—and peril—of the new technology.
How does CRISPR work?
Traditional gene therapy works via a relatively brute-force method of gene transfer. A harmless virus, or some other form of so-called vector, ferries a good copy of a gene into cells that can compensate for a defective gene that is causing disease. But CRISPR can fix the flawed gene directly, by snipping out bad DNA and replacing it with the correct sequence. In principle, that should work much better than adding a new gene because it eliminates the risk that a foreign gene will land in the wrong place in a cell's genome and turn on a cancer gene. And a CRISPR-repaired gene will be under the control of that gene’s natural promoter, so the cell won’t make too much or too little of its protein product.
What has CRISPR accomplished so far?
Researchers have published successes with using CRISPR to treat animals with an inherited liver disease and muscular dystrophy, and there will be more such preclinical reports at this week’s annual meeting of the American Society of Gene and Cell Therapy (ASGCT). The buzz around CRISPR is growing. This year’s meeting includes 93 abstracts on CRISPR (of 768 total), compared with only 33 last year. What’s more, investors are flocking to CRISPR. Three startups, Editas Medicine, Intellia Therapeutics, and CRISPR Therapeutics, have already attracted hundreds of millions of dollars.
So why isn’t CRISPR ready for prime time?
CRISPR still has a long way to go before it can be used safely and effectively to repair—not just disrupt—genes in people. That is particularly true for most diseases, such as muscular dystrophy and cystic fibrosis, which require correcting genes in a living person because if the cells were first removed and repaired then put back, too few would survive. And the need to treat cells inside the body means gene editing faces many of the same delivery challenges as gene transfer—researchers must devise efficient ways to get a working CRISPR into specific tissues in a person, for example.
CRISPR also poses its own safety risks. Most often mentioned is that the Cas9 enzyme that CRISPR uses to cleave DNA at a specific location could also make cuts where it’s not intended to, potentially causing cancer.
With these caveats, do you even need CRISPR?
Conventional gene addition treatments for some diseases are so far along that it may not make sense to start over with CRISPR. In Europe, where one gene therapy is already approved for use for a rare metabolic disorder, regulators are poised to approve a second for an immune disorder known as adenosine deaminase–severe combined immunodeficiency (SCID). And in the United States, a company this year expects to seek approval for a gene transfer treatment for a childhood blindness disease called Leber congenital amaurosis (LCA).
At the ASCGT meeting, researchers working with the company Bluebird Bio will present interim data for a late-stage trial showing that gene addition can halt the progression of cerebral adrenoleukodystrophy, a devastating childhood neurological disease. Final results could help pave the way for regulatory approval. Bluebird will also report on trials using gene transfer for two blood disorders, sickle cell disease and β-thalassemia, bringing these treatments closer to the clinic.
Except for LCA, in which gene-carrying viruses are injected directly into eyes, these diseases are treated by removing bone marrow cells from patients, adding a gene to the cells, and reinfusing the cells back into the patient. New, safer viral vectors have reduced risks of leukemia seen in a few patients in some early trials for immunodeficiency diseases. Researchers are seeing “excellent clinical responses,” says Donald Kohn of the University of California, Los Angeles.
Although Kohn and other researchers have used an older gene-editing tool known as zinc finger nucleases to repair defective genes causing sickle cell disease and a type of SCID in cells in a dish, only a tiny fraction of immature blood cells needed for the therapy to work end up with the gene corrected—far below the fraction altered by now standard gene transfer methods. One reason is because the primitive blood cells aren’t dividing much (more on this below). Because gene-editing methods such as CRISPR are so much less efficient than gene addition, for several diseases, “I don’t think there will be a strong rationale for switching to editing,” says Luigi Naldini of the San Raffaele Telethon Institute for Gene Therapy in Milan, Italy.
CRISPR also has other issues
Using CRISPR to cut out part of a gene—not correct the sequence—is relatively easy to do. In fact, this strategy is already being tested with zinc finger nucleases in a clinical effort to stop HIV infection. In this treatment, the nucleases are used to knock out a gene for a receptor called CCR5 in blood cells that HIV uses to get into cells.
But when CRISPR is used to correct a gene using a strand of DNA that scientists supply to cells, not just to snip out some DNA, it doesn’t work very well. That’s because the cells must edit the DNA using a process called homology-directed repair, or HDR, that is only active in dividing cells. And unfortunately, most cells in the body—liver, neuron, muscle, eye, blood stem cells—are not normally dividing. For this reason, “knocking out a gene is a lot simpler than knocking in a gene and correcting a mutation,” says Cynthia Dunbar, president-elect of ASGCT and a gene therapy researcher at the National Heart, Lung, and Blood Institute in Bethesda, Maryland.
Researchers are working on ways to get around this limitation. The genes for HDR are present in all cells, and it’s a matter of turning them on, perhaps by adding certain drugs to the cells, says CRISPR researcher Feng Zhang of the Broad Institute in Cambridge, Massachusetts. Another avenue is to find alternatives to the Cas9 system that don’t rely on the HDR process, Zhang says.
But the low rate of HDR in most cells is one reason why the first use of CRISPR in the clinic will likely involve disrupting genes, not fixing them. For example, several labs have shown in mice that CRISPR can remove a portion of the defective gene that causes Duchenne muscular dystrophy, so that the remaining portion will produce a functional, albeit truncated protein. Editas hopes to start a clinical trial next year to treat a form of LCA blindness by chopping out part of the defective gene. One proposed gene-editing treatment for sickle cell disease would similarly snip out some DNA, so that blood cells produce a fetal form of the oxygen-carrying protein hemoglobin.
And CRISPR still has big safety risks
The most-discussed safety risk with CRISPR is that the Cas9 enzyme, which is supposed to slice a specific DNA sequence, will also make cuts in other parts of the genome that could result in mutations that raise cancer risk. Researchers are moving quickly to make CRISPR more specific. For example, in January, one lab described a tweak to Cas9 that dramatically reduces off-target effects. And in April in Nature, another team showed how to make the enzyme more efficient at swapping out single DNA bases.
But immediate off-target cuts aren’t the only worry. Although it’s possible to deliver CRISPR’s components into cells in a dish as proteins or RNA, so far researchers can usually only get it working in tissue inside the body by using a viral vector to deliver the DNA for Cas9 into cells. This means that even after Cas9 has made the desired cuts, cells will keep cranking it out. “The enzyme will still hang around over 10, 20 years,” Zhang says. That raises the chances that even a very specific Cas9 will still make off-target cuts and that the body will mount an immune response to the enzyme.
This may not truly be a problem, Zhang suggests. His team created a mouse strain that is born with the gene for Cas9 turned on all the time, so it expresses the enzyme in all cells for the animal’s entire life. Even after interbreeding these mice for about 20 generations, the mice “seem to be fine” with no obvious abnormal health effects, Zhang says. All the same, “the most ideal case is, we want to shut off the enzyme.” And that may mean finding nonviral methods for getting Cas9 into cells, such as ferrying the protein with lipids or nanoparticles—delivery methods that biologists have long struggled to make work in living animals.
Other long-standing obstacles to gene therapy will confront efforts using CRISPR, too. Depending on the disease, any gene-edited cells may eventually die and patients could have to be treated multiple times. Researchers using gene transfer and editing approaches are also both hindered by limits on how much DNA a viral vector can carry. Right now CRISPR researchers often must use two different viruses to get CRISPR’s components into cells, which is less efficient than a single vector.
So what’s the bottom line?
Gene therapists remain excited by CRISPR, in part because it could tackle many more inherited diseases than can be treated with gene transfer. Among them are certain immune diseases where the amount of the repaired protein must be precisely controlled. In other cases, such as sickle cell disease, patients won’t get completely well unless a defective protein is no longer made by their cells, so just adding a gene isn’t enough. “It opens up a lot of diseases to gene therapy because gene addition wasn’t going to work,” Dunbar says.
After more than 2 decades of seeing their field through ups and downs, veterans of the gene therapy field are wary of raising expectations about CRISPR for treating diseases. “Whenever there’s a new technology, there’s a huge amount of excitement and everybody thinks it will be ready tomorrow to cure patients,” says gene therapy researcher Mark Kay of Stanford University in Palo Alto, California. “It’s going to take some time.”
The cyanobacterial hepatotoxin microcystin is assembled at a non-ribosomal peptide synthetase (NRPS) complex. The enormous structural diversity of this peptide, which is also found in closely related strains, is the result of frequent recombination events and point mutations. Here, we have compared the in vitro activation profiles of related monospecific and multispecific modules that either strictly incorporate leucine or arginine or incorporate chemically diverse amino acids in parallel into microcystin. By analyzing di- and tri-domain proteins we have dissected the role of adenylation and condensation domains for substrate specificity. We have further analyzed the role of subdomains and provide evidence for an extended gatekeeping function for the condensation domains of multispecific modules. By reproducing natural point mutations, we could convert a monospecific module into a multispecific module. Our findings may inspire novel synthetic biology approaches and demonstrate how recombination platforms of NRPSs have developed in nature.
n 2013, 5 exabytes of content were created each day, that is 5 x 10^18, or five quintillion bytes or 1000000000000000000B! – every day! and the amount is only increasing.
How we store this information is becoming a big challenge.
Storage of information in DNA is proposed as one solution. The idea has been around for a long time (first recorded in the USSR in the 1960s), but has only really begun to take off with the fall in price of DNA synthesis. One of the first major examples of synthetic DNA data storage was performed by George Church’s lab in 2012. On Jake Beal’s blog he reports from a two-day workshop investigating the latest prospects and challenges for an exciting field.
London designer and researcher Shamees Aden is developing a concept for running shoes that would be 3D-printed from synthetic biological material and could repair themselves overnightThe Protocell trainer would be 3D-printed to the exact size of...
n a crowded stretch of Flatbush Avenue in Brooklyn, on the seventh floor of a building gentrification forgot, is a place where you can dabble in genetic engineering. Genspace, a kind of co-working lab for scientists, offers a fully equipped research laboratory available for public use for a modest monthly fee.
It was the first of its kind to open its doors back in 2010 and signaled the rebirth of the gentleman (or gentlewoman) scientist. Since then, BioCurious, another DIY lab, has opened in Silicon Valley, allowing hobbyist biologists to fiddle with their own DNA and titrate their own blood samples. A number of startups like Bento Lab have popped up to serve the DIY Bio movement, making compact desktop versions of traditional biology lab equipment small enough to set up anywhere at home.
Above the din of rumbling trucks and screaming teenagers strolling home from nearby schools, the noise in the Genspace lab that is troubling founder Ellen Jorgensen is a centrifuge. It’s too loud and she is not sure if it is safe to use. The equipment in the lab was donated or purchased secondhand to keep costs down.
Biohackers push life to the limits with DIY biology Read more In one corner near the communal table that serves as an office sits a small aquarium of the type that usually houses hamsters in elementary schools. It is now home to a few enormous South American cockroaches. A DIY neuroscience company called Backyard Brains used to teach workshops at the lab using a SpikerBox, a device that picks up and displays nerve signals. The easiest way to show those nerve signals is to tear the leg off one of the roaches, attach it to the SpikerBox and stimulate it to show the nerve signals being sent from the leg on an app. Backyard Brains has not run the workshop in a while so the lab inherited the roaches, which Jorgensen has become attached to since she started feeding them. They’re practically pets at this point. “I don’t know how I would feel about the legs coming off,” she says.
Many different people have rotated through the lab, from those needing gel electrophoresis equipment to others looking for low-temperature storage. There are people working on an RNA-based therapy, on genetically engineering E coli to produce cellulose, on trying to turn spent grain from the brewing industry into feed using a fungus and on stabilization work for personal care products. While lab members are all adults, teenagers rotate through as well for science projects and internships.
One aim of synthetic biologists is to create novel and predictable biological systems from simpler modular parts. This approach is currently hampered by a lack of well-defined and characterised parts and devices. However, there is a wealth of existing biological information, which can be used to identify and characterise biological parts, and their design constraints in the literature and numerous biological databases. However, this information is spread amongst these databases in many different formats. New computational approaches are required to make this information available in an integrated format that is more amenable to data mining. A tried and tested approach to this problem is to map disparate data sources into a single dataset, with common syntax and semantics, to produce a data warehouse or knowledge base. Ontologies have been used extensively in the life sciences, providing this common syntax and semantics as a model for a given biological domain, in a fashion that is amenable to computational analysis and reasoning. Here, we present an ontology for applications in synthetic biology design, SyBiOnt, which facilitates the modelling of information about biological parts and their relationships. SyBiOnt was used to create the SyBiOntKB knowledge base, incorporating and building upon existing life sciences ontologies and standards. The reasoning capabilities of ontologies were then applied to automate the mining of biological parts from this knowledge base. We propose that this approach will be useful to speed up synthetic biology design and ultimately help facilitate the automation of the biological engineering life cycle.
Synthetic constructs in biotechnology, biocomputing, and modern gene therapy interventions are often based on plasmids or transfected circuits which implement some form of "on-off" switch. For example, the expression of a protein used for therapeutic purposes might be triggered by the recognition of a specific combination of inducers (e.g., antigens), and memory of this event should be maintained across a cell population until a specific stimulus commands a coordinated shut-off. The robustness of such a design is hampered by molecular ("intrinsic") or environmental ("extrinsic") noise, which may lead to spontaneous changes of state in a subset of the population and is reflected in the bimodality of protein expression, as measured for example using flow cytometry. In this context, a "majority-vote" correction circuit, which brings deviant cells back into the required state, is highly desirable, and quorum-sensing has been suggested as a way for cells to broadcast their states to the population as a whole so as to facilitate consensus. In this paper, we propose what we believe is the first such a design that has mathematically guaranteed properties of stability and auto-correction under certain conditions. Our approach is guided by concepts and theory from the field of "monotone" dynamical systems developed by M. Hirsch, H. Smith, and others. We benchmark our design by comparing it to an existing design which has been the subject of experimental and theoretical studies, illustrating its superiority in stability and self-correction of synchronization errors. Our stability analysis, based on dynamical systems theory, guarantees global convergence to steady states, ruling out unpredictable ("chaotic") behaviors and even sustained oscillations in the limit of convergence. These results are valid no matter what are the values of parameters, and are based only on the wiring diagram. The theory is complemented by extensive computational bifurcation analysis, performed for a biochemically-detailed and biologically-relevant model that we developed. Another novel feature of our approach is that our theorems on exponential stability of steady states for homogeneous or mixed populations are valid independently of the number N of cells in the population, which is usually very large (N ≫ 1) and unknown. We prove that the exponential stability depends on relative proportions of each type of state only. While monotone systems theory has been used previously for systems biology analysis, the current work illustrates its power for synthetic biology design, and thus has wider significance well beyond the application to the important problem of coordination of toggle switches.
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