Genetically encoded fluorescent biosensors allow researchers to see how products form in real time in microorganisms, and to test billions of candidates at a time
Synthetic biologists are learning to turn microbes and unicellular organisms into highly productive factories by re-engineering their metabolism to produce valued commodities such as fine chemicals, therapeutics and biofuels. To speed up identification of the most efficient producers, researchers at Harvard’s Wyss Institute for Biologically Inspired Engineering describe new approaches to this process and demonstrate how genetically encoded fluorescent biosensors can enable the generation and testing of billions of individual variants of a metabolic pathway in record time. The discussion and findings are reported in Trends in Biotechnology and the Proceedings of the National Academy of Sciences (PNAS).
Biotechnologists that tinker with the metabolism of microorganisms to produce valued products look at the engineering process through the lens of the so-called ‘design-build-test cycle.’ The idea is that multiple iterations of this cycle ultimately allow the identification of combinations of genetic and metabolic elements that produce the highest levels of a desired drug or chemical. Key to the cycle’s efficiency, however, is the ability to construct and test the largest number of variants possible; in the end, only a few of these variants will produce the product in industrially attractive amounts.
In the Trends in Biotechnology article, Wyss Institute scientists George Church, Ph.D., and Jameson Rogers, Ph.D., lay out the current state-of-the-art for designing, building and testing many variants at a time, a methodology that bioengineers call ‘multiplexing’. Church is a Wyss Institute Core Faculty member and Professor of Genetics at Harvard Medical School and Rogers, currently with the Boston Consulting Group, performed his work as a Harvard Pierce Fellow and Doctoral Student mentored by Church.
Bioengineers thoroughly understand how metabolic pathways work on the biochemical level and have a plethora of DNA sequences encoding variants of all of the necessary enzymes at their disposal. Deploying these sequences with the help of computational tools and regulating their expression with an ever-growing number of genetic elements, gives them access to an almost infinite pool of design possibilities. Similarly, revolutionary advances in technologies enabling DNA synthesis and manipulation have made the construction of billions of microorganisms, each containing a distinct design variant, a routine process.
“The real bottleneck in achieving high-throughput engineering cycles lies in the testing step. Current technology limits the number of designs scientists can evaluate to hundreds, or maybe even a thousand, different designs per day. Often the assays necessary are painstaking and prone to user error,” said Rogers.
Church and Rogers discuss how genetically encoded biosensors can help bioengineers overcome this hurdle. Such biosensors work by coupling the amount of a desired product produced within a microorganism to the expression of an antibiotic resistance gene such that only high producers survive. Alternatively, the expression of a fluorescent protein can be used for high-speed sorting of rare but highly productive candidates from large populations of less productive microbes.
“Now, by having developed both types of genetically encoded biosensors we can close the loop of a fully multiplexed engineering cycle. This enables exploration of design spaces for specific metabolic pathways in much greater breadth and depth. Fluorescent biosensors, in particular, enable a brand new type of pipeline engineering in which we can observe metabolic product levels at all times during the process with extraordinary sensitivity and ability to further manipulate the engineering cycle,” said Church.
Earlier work by Church’s team at the Wyss Institute already demonstrated that the levels of commercially valuable chemicals produced by bacteria could be raised through several rounds of a design-build-test cycle that employed an antibiotic selection-based biosensor. Now, Church and Rogers report in PNAS the unique advantages that fluorescent biosensors provide to bioengineers.
“Our fluorescent biosensors are built around specialized proteins that directly sense commercially valuable metabolites. These sensor proteins switch on the expression of a fluorescent reporter protein, resulting in cellular brightness that is proportional to the amount of chemical produced within the engineered cells. We can literally watch the biological production of valuable chemicals in real-time as the synthesis occurs and isolate the highest producers out of cultures with billions of candidates,” said Rogers, who was named one of Forbes’ “30 Under 30” in Science for opening new perspectives in bioengineering.
Using this strategy, the Wyss researchers have established fluorescent biosensors for the production of super-absorbent polymers and plastics like the coveted acrylate from which a range of products is made. In fact, the study established the first engineered pathway able to biologically produce acrylate from common sugar, rather than the previously required petroleum compounds.
“This newly emerging biosensor technology has the potential to transform metabolic engineering in areas ranging from industrial manufacturing to medicine, and it can have a positive impact on our environment by making the production of drugs and chemicals independent from fossil fuels,” said Wyss Institute Founding Director Donald Ingber, M.D., Ph.D., who is the Judah Folkman Professor of Vascular Biology at HMS and the Vascular Biology Program at Boston Children’s Hospital, as well as Professor of Bioengineering at the Harvard John A. Paulson School of Engineering and Applied Sciences.
The Latest on: Metabolic engineering
via Google News
The Latest on: Metabolic engineering
- Eliciting the impacts of cellular noise on metabolic trade-offs by quantitative mass imaging on February 19, 2019 at 2:30 am
Optimal metabolic trade-offs between growth and productivity are key constraints in strain optimization by metabolic engineering; however, how cellular noise impacts these trade-offs and drives the em... […]
- A comprehensive metabolic map for production of bio-based chemicals on January 16, 2019 at 5:41 am
The team was led by Distinguished Professor Sang Yup Lee, who has produced high-quality metabolic engineering and systems engineering research for decades, and made the hallmark chemicals map ... […]
- Plants metabolically engineered to produce new drugs on November 3, 2018 at 5:00 pm
Scientists have been engineering new genes into plants for a number of years in an effort to expand on naturally occurring medicinal compounds. Now chemists at MIT have gone one step further, using an ... […]
- Metabolic engineering of plants for sustainable chemicals on October 28, 2018 at 8:14 am
The position will employ the power of systems biology to investigate metabolic pathways in photosynthetic organisms to engineer the efficient conversion of carbon dioxide and sunlight into valuable ch... […]
- Metabolic engineering of E. coli for the secretory production of free haem on August 29, 2018 at 6:55 am
Researchers of KAIST have defined a novel strategy for the secretory production of free haem using engineered Escherichia coli (E. coli) strains. They utilized the C5 pathway, the optimized downstream ... […]
- Yield10 Addresses Application of Metabolic Engineering to Increase Crop Yield in Paper Published in Plant Science on April 26, 2018 at 1:30 am
Chief Science Officer Kristi Snell also confirmed as a keynote speaker at upcoming plant meeting WOBURN, Mass., April 26, 2018 (GLOBE NEWSWIRE) -- Yield10 Bioscience, Inc. (NASDAQ:YTEN), a Company dev... […]
- Yield10 Addresses Application of Metabolic Engineering to Increase Crop Yield in Paper Published in Plant Science on April 25, 2018 at 5:00 pm
April 26, 2018 08:30 ET | Source: Yield10 Bioscience, Inc. Chief Science Officer Kristi Snell also confirmed as a keynote speaker at upcoming plant meeting WOBURN, Mass., April 26, 2018 (GLOBE NEWSWIR... […]
- Metabolic engineering of Ustilago trichophora: an isotope-assisted metabolomics approach for the improvement of malate production from glycerol on January 31, 2018 at 4:00 pm
Biodiesel production is usually accompanied by the production of 10% (w/v) glycerol as main low-value by-product, making it not yet economically competitive to petroleum-based processes. Recently, Ust... […]
- NSF awards grant to DMC Biotechnologies for high throughput metabolic engineering platform development. on November 9, 2017 at 11:04 pm
In Colorado, DMC Biotechnologies was awarded a National Science Foundation Small Business Innovation Research Phase II grant for $600,000 to commercialize their proprietary high throughput metabolic e... […]
- Metabolic Regulation and Metabolic Engineering for Biofuel and Biochemical Production on April 26, 2017 at 1:03 pm
Despatched in 2 business days. The global warming problem is becoming critical year by year, causing climate disaster all over the world, where it has been believed that the CO2 gas emitted from the f... […]
via Bing News