by Benjamin Reeve, Theo Sanderson, Tom Ellis, Paul Freemont
"As our understanding of natural biological systems grows, so too does our ability to alter and rebuild them. Synthetic biology is the application of engineering principles to biology in order to design and construct novel biological systems for specific applications. Bioluminescent organisms offer a treasure trove of light-emitting enzymes that may have applications in many areas of bioengineering, from biosensors to lighting. A few select bioluminescent organisms have been well researched and the molecular and genetic basis of their luminescent abilities elucidated, with work underway to understand the basis of luminescence in many others. Synthetic biology will aim to package these light-emitting systems as self-contained biological modules, characterize their properties, and then optimize them for use in other chassis organisms. As this catalog of biological parts grows, synthetic biologists will be able to engineer complex biological systems with the ability to emit light. These may use luminescence for an array of disparate functions, from providing illumination to conveying information or allowing communication between organisms."
"Soon to be grown for ornamental use only.Credit: Mark Nesbitt and Samuel Delwen, CC BY
By Luc Henry, Swiss Federal Institute of Technology in Lausanne
The past few decades have seen enormous progress being made in synthetic biology – the idea that simple biological parts can be tweaked to do our bidding. One of the main targets has been hacking the biological machinery that nature uses to produce chemicals. The hope is – once we understand enough – we might be able to design processes that convert cheap feedstock, such as sugar and amino acids, into drugs or fuels. These production lines can then be installed into microbes, effectively turning living cells into factories.
Taking a leap in that direction, researchers from Stanford University have created a version of baker’s yeast (Saccharomyces cerevisiae) that contains genetic material of the opium poppy (Papaver somniferum), bringing the morphine microbial factory one step closer to reality. These results published in the journal Nature Chemical Biology represent a significant scientific success, but eliminating the need to grow poppies may still be years away.
More than bread and booze
If dog has been man’s best friend for thousands of years or more, the humble yeast has long been man’s second-best friend. The single-cell organism has been exploited by human societies to produce alcoholic beverages or bread for more than 4,000 years.
Like any animal or plant that mankind domesticated, there has been a particular interest in the study and optimisation of yeast. When breeding turned into a scientific discipline, it quickly became a model organism for biological experiments. And in 1996, its complete genome was the first sequenced from a eukaryotic organism – the more advanced tree of life. This extensive knowledge of yeast biology makes it an attractive platform for synthetic biology.
In the new study, Christina Smolke and her team further show that yeast could be a good candidate for the production of opioids – a class of drugs that includes morphine. To achieve this transformation, Smolke would need a complete biological pathway required to produce complex opioids.
In 2008 she got the first hint on successfully fermenting simple sugars to make salutaridine, an opioid precursor. Then in 2010, a Canadian team identified the last two missing pieces of the morphine puzzle in the genome of opium poppy.
Using these biological parts from plants, together with some from bacteria, Smolke has now created yeast that can produce many natural and unnatural opioids. All it takes is to feed the microbes an intermediary molecule extracted from the poppy plant called thebaine.
These results bring the technology one step closer to microbial factories that can produce pharmaceutical molecules in a tank rather than in the field. What is left now is for Smolke to find a way to turn salutaridine into thebaine efficiently. Filling this gap may allow her to create a yeast strain producing opioids directly from sugars.
Teaching yeast new tricks
There have been other synthetic biology landmarks in the past. In 2006, chemical engineer Jay Keasling of the University of California at Berkeley and his team successfully introduced genetic material from the sweet wormwood plant (Artemisia annual) into yeast. Their microbial factory was able to produce artemisinic acid, which is only one chemical step away from artemisinin, the most efficient drug against Plasmodium falciparum malaria...."
"Synthetic Biology is an engineering discipline where parts of DNA sequences are composed into novel, complex systems that execute a desired biological function. Functioning and well-behaving biological sys- tems adhere to a certain set of biological “rules”. Data exchange standards and Bio-Design Automation (BDA) tools support the organization of part libraries and the exploration of rule-compliant compositions. In this work, we formally define a design specification language, enabling the integration of biological rules into the Synthetic Biology engineering process. The supported rules are divided into five categories: Counting, Pairing, Positioning, Orientation, and Interactions. We formally define the semantics of each rule, charac- terize the language’s expressive power, and perform a case study in that we iteratively design a genetic Priority Encoder circuit following two alternative paradigms — rule-based and template-driven. Ultimately, we touch a method to approximate the complexity and time to computationally enumerate all rule-compliant designs. Our specification language may or may not be expressive enough to capture all designs that a Syn- thetic Biologist might want to describe, or the complexity one might find through experiments. However, computational support for the acquisition, specification, management, and application of biological rules is inevitable to understand the functioning of biology. "
We like to think that all our smarts are contained in our brain, but researchers at Umea University in Sweden have found that the neurons that extend into our fingertips perform the same sorts of calculations that take place in the cerebral cortex.
Whither thou goest, synthetic biology? First, let's put aside the dystopian scenarios of nasty modified viruses escaping from the fermentor Junior has jury-rigged in his bedroom lab. Designing virulent...
Slate Magazine (blog) No One Should be Afraid of Synthetic Biology-Produced Vanilla Slate Magazine (blog) Perls also writes, “Like 'traditional' GMOs, synthetic biology ingredients are entering food and consumer products in absence of adequate...
This event will feature important advances in synbio from leading companies in the field, ranging from industrial to healthcare applications. (RT @AmyElizaTayler: I'm going to the @IChemE SynBio symposium on 22nd Sept.
Discover Magazine (blog) Instead of Poppies, Engineering Microbes to Make Morphine Discover Magazine (blog) The past few decades have seen enormous progress being made in synthetic biology – the idea that simple biological parts can be tweaked to...
I think this can be used to build the decentralized company structure for CytoComp. Moreover, this will be great for sharing of e.g. DNA sequencing data in a secure way and to build a decentralized applications suitable for CytoComp.
Thus I am exploring this subject by doing the following project, which will give me insight how the platform works:
The Human Frontier Science Program Organization has announced that the 2015 HFSP Nakasone Award has been conferred upon James Collins of Boston University and Harvard's Wyss Institute for his innovative work on synthetic gene networks and programmable cells which launched the exciting field of synthetic biology.
"In principle, this is a technology that could enable correction of genetic mutations that would otherwise lead to disease," said Doudna, a professor of chemistry and biochemistry and molecular biology, in a telephone interview.
This is a group for people interested in Synthetic Biology and open technologies: the DNA-based reprogramming and computational modelling of living systems and low-cost hardware for biological instrum (Thanks to a flexible Café Synthetique ...