Institute of Biological Chemistry, Academia Sinica
liaoj@as.edu.tw
+886-2-27855696
Our research has focused on metabolism, including its biochemistry, evolution, and regulation. We use metabolic engineering, synthetic biology, and evolutionary engineering to construct microorganisms and plants to assimilate greenhouse gases to address the climate change problem and advance bioenergy applications. We also develop mathematical tools for investigating metabolism and guiding engineering design.
Currently, our main projects include engineering proteins, biochemical pathways, microorganisms, and plants for CO2 fixation and methane and methanol conversion. Our ultimate goal is to use biochemical methods to replace petroleum processing.
Recent publications:
Dual-cycle CO2 fixation enhances growth and lipid synthesis in Arabidopsis thaliana
Free Download
Kuan-Jen Lu, Chia-Wei Hsu, Wann-Neng Jane, Mien-Hao Peng, Ya-Wen Chou, Pin-Hsuan Huang, Kuo-Chen Yeh, Shu-Hsing Wu, James C Liao
Science 389 (6765), eadp3528 DOI: 10.1126/science.adp3528
Carbon fixation through the Calvin-Benson-Bassham (CBB) cycle accounts for the majority of carbon dioxide (CO2) uptake from the atmosphere. The CBB cycle generates C3 carbohydrates but is inefficient at producing acetyl–coenzyme A (CoA) (C2), which is the universal precursor for synthesizing lipids. In this work, we introduced in Arabidopsis thaliana a new-to-nature CO2 fixing cycle, malyl-CoA-glycerate (McG) cycle, which together with the CBB cycle forms a dual cycle CO2 fixation system. This cycle can fix one additional carbon by phosphoenolpyruvate carboxylase and convert the photorespiration product, glycolate, to acetyl-CoA. Plants with the McG cycle show enhanced protein abundance in their photosystems and enhanced photosystem II efficiency. McG plants had doubled CO2 fixation rates under atmospheric CO2, increased lipid production, pronounced growth enhancement, and tripled the seed yield.
Evolutionary engineering of methylotrophic E. coli enables fast growth on methanol
LY Nieh, FYH Chen, HW Jung, KY Su, CY Tsuei, CT Lin, YQ Lee, JC Liao
Nature Communications 15 (1), 8840 DOI: 10.1038/s41467-024-53206-4
As methanol can be derived from either CO2 or methane, methanol economy can play an important role in combating climate change. In this scenario, rapid utilization of methanol by an industrial microorganism is the first and crucial step for efficient utilization of the C1 feedstock chemical. Here, we report the development of a methylotrophic E. coli strain with a doubling time of 3.5 hours under optimal conditions, comparable or faster than native model methylotrophs Methylorubrum extorquens AM1 (Td~4hr) and Bacillus methanolicusat 37°C (Td~5hr). To accomplish this, we develop a bacterial artificial chromosome (BAC) with dynamic copy number variation (CNV) to facilitate overcoming the formaldehyde-induced DNA-protein cross-linking (DPC) problem in the evolution process. We track the genome variations of 75 cultures along the evolution process by next-generation sequencing, and identified the features of the fast-growing strain. After stabilization, the final strain (SM8) grows to 20 g/L of cell mass within 77 hrs in a bioreactor. This study illustrates the potential of dynamic CNV as an evolution tool and syntheticmethylotrophs as a platform for sustainable biotechnological applications.
An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria
KJ Lu, CW Chang, CH Wang, FYH Chen, IY Huang, PH Huang, CH Yang, ...
Nature Metabolism 5 (7), 1111-1126 DOI: 10.1038/s42255-023-00831-w
Regulation of CO2 fixation in cyanobacteria is important both for the organism and global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 (SeXPK) possesses a distinct ATP-sensing mechanism, where a drop in ATP level allows SeXPK to divert precursors of the RuBisCO substrate away from the Calvin–Benson–Bassham cycle. Deleting the SeXPK gene increased CO2 fixation particularly during light–dark transitions. In high-density cultures, the Δxpk strain showed a 60% increase in carbon fixation and unexpectedly resulted in sucrose secretion without any pathway engineering. Using cryo-EM analysis, we discovered that these functions were enabled by a unique allosteric regulatory site involving two subunits jointly binding two ATP, which constantly suppresses the activity of SeXPK until the ATP level drops. This magnesium-independent ATP allosteric site is present in many species across all three domains of life, where it may also play important regulatory functions.
A cell-free self-replenishing CO2-fixing system
S Luo, PP Lin, LY Nieh, GB Liao, PW Tang, C Chen, JC Liao
Nature Catalysis 5 (2), 154-162 DOI:10.1038/s41929-022-00746-x
Biological CO2 fixation is so far the most effective means for CO2 reduction at scale and accounts for most of the CO2 fixed on Earth. Through this process, carbon is fixed in cellular components and biomass during organismal growth. To uncouple CO2 fixation from growth and cellular regulation, cell-free CO2 fixation systems represent an alternative approach since the rate can be independently manipulated. Here we designed an oxygen-insensitive, self-replenishing CO2 fixation system with opto-sensing. The system comprises a synthetic reductive glyoxylate and pyruvate synthesis (rGPS) cycle and the malyl-CoA-glycerate (MCG) pathway to produce acetyl-coenzyme A (CoA), pyruvate and malate from CO2, which are also intermediates in the cycle. We solved various problems associated with the in vitro system, and implemented opto-sensing modules to control the regeneration of cofactors. We accomplished sustained operation for 6 hours with a CO2-fixing rate comparable to or greater than typical CO2 fixation rates of photosynthetic or lithoautotrophic organisms.
Converting Escherichia coli to a synthetic methylotroph growing solely on methanol
FYH Chen, HW Jung, CY Tsuei, JC Liao
Cell 182 (4), 933-946. e14 DOI:10.1016/j.cell.2020.07.010
Methanol, being electron rich and derivable from methane or CO2, is a potentially renewable one-carbon (C1) feedstock for microorganisms. Although the ribulose monophosphate (RuMP) cycle used by methylotrophs to assimilatemethanol differs from the typical sugar metabolism by only three enzymes, turning a non-methylotrophic organism to a synthetic methylotroph that grows to a high cell density has been challenging. Here we reprogrammed E. coli using metabolic robustness criteria followed by laboratory evolution to establish a strain that can efficiently utilize methanol as the sole carbon source. This synthetic methylotroph alleviated a so far uncharacterized hurdle, DNA-protein crosslinking (DPC), by insertion sequence (IS)-mediated copy number variations (CNVs) and balanced the metabolic flux by mutations. Being capable of growing at a rate comparable with natural methylotrophs in a wide range of methanol concentrations, this synthetic methylotrophic strain illustrates genome editing and evolution for microbial tropism changes and expands the scope of biological C1 conversion.
DEGREES
POSITIONS HELD
AWARDS / HONORS
Dual-cycle CO2 fixation enhances growth and lipid synthesis in Arabidopsis thaliana.
Lu KJ, Hsu CW, Jane WN, Peng MH, Chou YW, Huang PH, Yeh KC, Wu SH, Liao JC
Science (2025)
Evolutionary engineering of methylotrophic E. coli enables fast growth on methanol.
Nieh LY, Chen FY, Jung HW, Su KY, Tsuei CY, Lin CT, Lee YQ, Liao JC
Nature Commun (2024)
An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria.
Lu KJ, Chang CW, Wang CH, Chen FY, Huang IY, Huang PH, Yang CH, Wu HY, Wu WJ, Hsu KC, Ho MC, Tsai MD, Liao JC
Nature Metabolism (2023)
A cell-free self-replenishing CO2-fixing system.
Luo S, Lin PP, Nieh LY, Liao GB, Tang PW, Chen C, Liao JC
Nature Catalysis (2022)
Converting Escherichia coli to a Synthetic Methylotroph Growing Solely on Methanol.
Chen FY, Jung HW, Tsuei CY, Liao JC
Cell (2020)
Metabolic repair through emergence of new pathways in Escherichia coli.
Pontrelli S, Fricke RCB, Teoh ST, Laviña WA, Putri SP, Fitz-Gibbon S, Chung M, Pellegrini M, Fukusaki E, Liao JC
Nature Chemical Biology (2018)
Synthetic Non-Oxidative Glycolysis Enables Complete Carbon Conservation.
Bogorad IW, Lin TS, Liao JC
Nature (2013)
Integrated electro-microbial conversion of CO2 to higher alcohols.
Li H, Opgenorth PH, Wernick DG, Rogers S, Wu TY, Higashide W, Malati P, Huo YX, Cho KM, Liao JC
Science (2012)
Non-Fermentative Pathways for Synthesis of Branched-Chain Higher Alcohols as Biofuels.
Atsumi S, Hanai T, Liao JC
Nature (2008)
A synthetic gene-metabolic oscillator.
Fung E, Wong WW, Suen JK, Bulter T, Lee SG, Liao JC
Nature (2005)
