Synthetic Biology Engineering Research Center

Emeryville, CA, United States

Synthetic Biology Engineering Research Center

Emeryville, CA, United States

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News Article | November 20, 2015
Site: www.biosciencetechnology.com

Magic tricks work because they take advantage of the brain’s sensory assumptions, tricking audiences into seeing phantoms or overlooking sleights of hand. Now a team of UC San Francisco researchers has discovered that even brainless single-celled yeast have sensory biases that can be hacked by a carefully engineered illusion, a finding that could be used to develop new approaches to fighting diseases such as cancer. “The ability to perceive and respond to the environment is a basic attribute of all living organisms, from the greatest to the smallest,” said Wendell Lim, PhD, the study’s senior author. “And so is the susceptibility to misperception. It doesn’t matter if the illusion is based on molecular sensors within a single cell or neurons in the brain.” In the new study, published online Nov. 19, 2015 in Science Express, Lim and his team discovered that yeast cells falsely perceive a specifically timed pattern of stress – caused by alternating between low and mildly increased sodium levels – as a massive, continuously increasing ramp of stress. In response, the microbes end up over-responding and killing themselves. The results, Lim said, suggest a whole new way of looking at the perceptual abilities of simple cells and could even be used to develop new approaches to fighting diseases using the power of illusion. “This discovery was a bit of an accident actually,” said Lim, chair of the Department of Cellular and Molecular Pharmacology at UCSF, director of the UCSF Center for Systems and Synthetic Biology, and a Howard Hughes Medical Institute (HHMI) investigator. “We were interested in the general issue of how cells interpret information over time. Frequency is a key aspect of all our communications, whether it’s hearing language or transmitting radio signals, but do cells themselves use this kind of information? It’s something we don’t know much about.” To explore this question, two postdoctoral fellows in Lim’s lab, Ping Wei, Ph.D., now at Peking University School of Life Sciences, and Amir Mitchell, Ph.D., set up a system that allowed them to expose yeast to a mild stressor – a small increase in salt in the yeast’s environment – and to oscillate between the increased salt level and the baseline level at different frequencies. Normally, sensor molecules in a yeast cell detect changes in salt concentration and instruct the cell to respond by producing a protective chemical. After this transient response, the cell can resume growing happily as if conditions had not changed. The researchers found that the cells were perfectly capable of adapting when they flipped the salt stress on and off every minute or every 32 minutes. But to their surprise, when they tried an eight-minute oscillation of precisely the same salt level the cells quickly stopped growing and began to die off. “That was just a jaw-dropping moment,” said Mitchell. “These cells should be able to handle this level of osmotic stress, but at one particular frequency they just go haywire. We’d never seen anything like this before.” Could sensory illusions be used to fight cancer? Mitchell, who was first author on the new study, went on to inspect the cellular mechanism underlying this unexpected, frequency-dependent toxicity. Using mathematical modeling and experiments in which he tweaked the molecular wiring of the mitogen activated protein kinase (MAPK) pathway that mediates the cells’ salt-sensing system, he revealed a sensory misperception: Because of the way the MAPK pathway is set up, the cells interpret an eight-minute oscillation as an ever-increasing staircase of salt concentration. This leads to excessive activation of the cells’ protective response, and ultimately to their death “Why would these cells have evolved this bizarre sensitivity to salt oscillations?” Mitchell asked. “Well, we don’t think that they did. It’s just a side effect of the fact that the molecular signaling network yeast cells use to mediate this stress response was optimized for their natural environment, in which salt stress normally occurs in a gradually increasing ramp – like if the yeast is sitting on a grape as morning dew slowly evaporates. It’s this assumption on the part of the yeast – their anticipation that the stress will keep getting more severe – that creates their Achilles heel.” The study suggests that many cell types, including human cells, may be predisposed to misperceptions and could be fooled by carefully engineered illusions. For instance, Mitchell said, the signaling pathway by which human cancer cells respond to chemical growth factors is closely related to the stress-sensing MAPK pathway in yeast. Thus, identification of cell-specific misperceptions might ultimately be exploited to induce cancer cells to kill themselves, he suggested, while minimally harming healthy, neighboring cells. “On its own, this is a humble finding,” Lim said, but he believes it has broader implications for biomedical research. “Like us, cells have biased perceptions based on what environmental patterns they’ve evolved with. By understanding these biases, we can modulate their behavior,” he said. “In particular, it’s striking to realize how important the time domain is for cells. The temporal pattern with which we present any stimulus, whether it’s salt concentrations, drugs or beams of light, may make all the difference.” The research was supported by the National Institutes of Health, the National Science Foundation (NSF) Synthetic Biology Engineering Research Center (SynBERC), HHMI, the Chinese Ministry of Science and Technology, the National Natural Science Foundation of China, the Peking-Tsinghua Center for Life Sciences, the European Molecular Biology Organization, and the UCSF Program for Breakthrough Biomedical Research (PBBR).


Zhang F.,Joint BioEnergy Institute | Zhang F.,Lawrence Berkeley National Laboratory | Zhang F.,University of California at Berkeley | Keasling J.,Joint BioEnergy Institute | And 3 more authors.
Trends in Microbiology | Year: 2011

Many metabolic pathways in microbial hosts have been created, modified and engineered to produce useful molecules. The titer and yield of a final compound is often limited by the inefficient use of cellular resources and imbalanced metabolism. Engineering sensory-regulation devices that regulate pathway gene expression in response to the environment and metabolic status of the cell have great potential to solve these problems, and enhance product titers and yields. This review will focus on recent developments in biosensor design, and their applications for controlling microbial behavior. © 2011.


Poust S.,University of California at Berkeley | Poust S.,Joint BioEnergy Institute | Hagen A.,University of California at Berkeley | Hagen A.,Joint BioEnergy Institute | And 7 more authors.
Current Opinion in Biotechnology | Year: 2014

Engineering modular polyketide synthases (PKSs) has the potential to be an effective methodology to produce existing and novel chemicals. However, this potential has only just begun to be realized. We propose the adoption of an iterative design-build-test-learn paradigm to improve PKS engineering. We suggest methods to improve engineered PKS design by learning from laboratory-based selection; adoption of DNA design software and automation to build constructs and libraries more easily; tools for the expression of engineered proteins in a variety of heterologous hosts; and mass spectrometry-based high-throughput screening methods. Finally, lessons learned during iterations of the design-build-test-learn cycle can serve as a knowledge base for the development of a single retrosynthesis algorithm usable by both PKS experts and non-experts alike. © 2014.


Yuzawa S.,University of California at Berkeley | Eng C.H.,University of California at Berkeley | Eng C.H.,Synthetic Biology Engineering Research Center | Katz L.,University of California at Berkeley | And 5 more authors.
Biochemistry | Year: 2013

LipPks1, a polyketide synthase subunit of the lipomycin synthase, is believed to catalyze the polyketide chain initiation reaction using isobutyryl-CoA as a substrate, followed by an elongation reaction with methylmalonyl-CoA to start the biosynthesis of antibiotic α-lipomycin in Streptomyces aureofaciens Tü117. Recombinant LipPks1, containing the thioesterase domain from the 6-deoxyerythronolide B synthase, was produced in Escherichia coli, and its substrate specificity was investigated in vitro. Surprisingly, several different acyl-CoAs, including isobutyryl-CoA, were accepted as the starter substrates, while no product was observed with acetyl-CoA. These results demonstrate the broad substrate specificity of LipPks1 and may be applied to producing new antibiotics. © 2013 American Chemical Society.


Poust S.,University of California at Berkeley | Phelan R.M.,Joint BioEnergy Institute | Deng K.,Joint BioEnergy Institute | Katz L.,Synthetic Biology Engineering Research Center | And 3 more authors.
Angewandte Chemie - International Edition | Year: 2015

The gem-dimethyl groups in polyketide-derived natural products add steric bulk, accordingly, lend increased stability to medicinal compounds, however, our ability to rationally incorporate this functional group in modified natural products is limited. In order to characterize the mechanism of gem-dimethyl group formation, with a goal toward engineering of novel compounds containing this moiety, the gem-dimethyl group producing polyketide synthase (PKS) modules of yersiniabactin and epothilone were characterized using mass spectrometry. The work demonstrated, contrary to the canonical understanding of reaction order in PKSs, that methylation can precede condensation in gemdimethyl group producing PKS modules. Experiments showed that both PKSs are able to use dimethylmalonyl acyl carrier protein (ACP) as an extender unit. Interestingly, for epothilone module 8, use of dimethylmalonyl-ACP appeared to be the sole route to form a gem-dimethylated product, while the yersiniabactin PKS could methylate before or after ketosynthase condensation. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA.


Yuzawa S.,University of California at Berkeley | Yuzawa S.,Joint BioEnergy Institute | Kim W.,University of California at Berkeley | Kim W.,Joint BioEnergy Institute | And 6 more authors.
Current Opinion in Biotechnology | Year: 2012

Heterologous production of polyketide compounds, an important class of natural products with complex chemical structures, was first demonstrated with Streptomyces parvulus in 1984. Although Streptomyces strains are good first options for heterologous polyketide biosynthesis, their slow growth kinetics prompt other hosts to also be considered. Escherichia coli provides key elements of an ideal host in terms of the growth rate, culture conditions, and available recombinant DNA tools. Here we review the current status and potential for metabolic engineering of polyketides in E. coli. © 2012.


Zhang F.,University of California at Berkeley | Zhang F.,Joint BioEnergy Institute | Zhang F.,Lawrence Berkeley National Laboratory | Rodriguez S.,University of California at Berkeley | And 4 more authors.
Current Opinion in Biotechnology | Year: 2011

Production of biofuels from renewable resources such as cellulosic biomass provides a source of liquid transportation fuel to replace petroleum-based fuels. This endeavor requires the conversion of cellulosic biomass into simple sugars, and the conversion of simple sugars into biofuels. Recently, microorganisms have been engineered to convert simple sugars into several types of biofuels, such as alcohols, fatty acid alkyl esters, alkanes, and terpenes, with high titers and yields. Here, we review recently engineered biosynthetic pathways from the well-characterized microorganisms Escherichia coli and Saccharomyces cerevisiae for the production of several advanced biofuels. © 2011 Elsevier Ltd.


Beller H.R.,Joint BioEnergy Institute | Lee T.S.,Joint BioEnergy Institute | Katz L.,Synthetic Biology Engineering Research Center
Natural Product Reports | Year: 2015

Covering: 2005 to 2015 Although natural products are best known for their use in medicine and agriculture, a number of fatty acid-derived and isoprenoid natural products are being developed for use as renewable biofuels and bio-based chemicals. This review summarizes recent work on fatty acid-derived compounds (fatty acid alkyl esters, fatty alcohols, medium- and short-chain methyl ketones, alkanes, α-olefins, and long-chain internal alkenes) and isoprenoids, including hemiterpenes (e.g., isoprene and isopentanol), monoterpenes (e.g., limonene), and sesquiterpenes (e.g., farnesene and bisabolene). © 2015 The Royal Society of Chemistry.


Leguia M.,University of California at Berkeley | Leguia M.,Synthetic Biology Engineering Research Center | Brophy J.,University of California at Berkeley | Densmore D.,Boston University | And 3 more authors.
Methods in Enzymology | Year: 2011

The primary bottleneck in synthetic biology research today is the construction of physical DNAs, a process that is often expensive, time-consuming, and riddled with cloning difficulties associated with the uniqueness of each DNA sequence. We have developed a series of biological and computational tools that lower existing barriers to automation and scaling to enable affordable, fast, and accurate construction of large DNA sets. Here we provide detailed protocols for high-throughput, automated assembly of BglBrick standard biological parts using iterative 2ab reactions. We have implemented these protocols on a minimal hardware platform consisting of a Biomek 3000 liquid handling robot, a benchtop centrifuge and a plate thermocycler, with additional support from a software tool called AssemblyManager. This methodology enables parallel assembly of several hundred large error-free DNAs with a 96+% success rate. © 2011 Elsevier Inc. All rights reserved.


Sanders R.,Synthetic Biology Engineering Research Center
Electronic Products | Year: 2013

A panel discussion held in Stanley Hall auditorium at the University of California Berkeley focused on a theme entitled 'Programming Life: the revolutionary potential of synthetic biology. Juan Enriquez, co-founder of the company Synthetic Genomics and keynote speaker, compared the digital revolution driven by considering information as a string of ones and zeros to the coming synthetic biology revolution based on thinking about life as a mix of interchangeable parts, such as genes and gene networks. The participants were informed that a Jay Keasling, a UC Berkeley chemical engineer and director of SynBERC, was playing a key role in developing the field of synthetic biology. Keasling was also CEO of the Joint BioEnergy Institute who was focused on converting microbes to turn a billion tons of biomass into fuel, producing a significant portion of the US's fuel needs.

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