genetic-engineering-an-unconventional-yeast-for-renewable-biofuel

Genetic Engineering of an Unconventional Yeast for Renewable Biofuel and Biochemical Production

Yarrowia lipolytica is a non-pathogenic, dimorphic and strictly aerobic yeast species. Owing to its distinctive physiological features and metabolic ...

National University of Singapore

Among various routes for the biological hydrogen production, the NAD(P)H-dependent pentose phosphate (PP) pathway is the most efficient for the dark fermentation. Few studies, however, have focused on the glucose-6-phosphate 1-dehydrogenase, encoded by zwf, as a key enzyme activating the PP pathway. Although the gluconeogenic activity is essential for activating the PP pathway, it is difficult to enhance the NADPH production by regulating only this activity because the gluconeogenesis is robust and highly sensitive to concentrations of glucose and AMP inside the cell. In this study, the FBPase II (encoded by glpX), a regulation-insensitive enzyme in the gluconeogenic pathway, was activated. Physiological studies of several recombinant, ferredoxin-dependent hydrogenase system-containing Escherichia coli BL21(DE3) strains showed that overexpression of glpX alone could increase the hydrogen yield by 1.48-fold compared to a strain with the ferredoxin-dependent hydrogenase system only; the co-overexpression of glpX with zwf increased the hydrogen yield further to 2.32-fold. These results indicate that activation of the PP pathway by glpX overexpression-enhanced gluconeogenic flux is crucial for the increase of NAD(P)H-dependent hydrogen production in E. coli BL21(DE3).

Engineering the pentose phosphate pathway to improve hydrogen yield in recombinant Escherichia coli.

Glycolysis has evolved to be a highly robust mechanism for maintaining the cellular metabolism of living organisms. However, relevant modifications of glycolytic activity are required to intentionally modulate cellular phenotypes. Here, we designed a platform that allows switching control of glycolysis in Escherichia coli in response to an environmental signal, in this case, temperature. This system functions by regulating the expression of gapA, which encodes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), one of the key glycolytic enzymes. Because a very low level of gapA expression is capable of maintaining cellular physiology, we also modified GAPDH through directed evolution to provide sensitive regulation of glycolytic activity. The switching control of glycolysis was successfully demonstrated by regulating the expression of engineered gapA through changes in temperature. This system offers potential control over the cell's central carbon-metabolism switch, providing the ability to perform reprogrammed tasks with desired timing depending on environmental signals.

Engineering glyceraldehyde-3-phosphate dehydrogenase for switching control of glycolysis in Escherichia coli.

Intravascular optical frequency-domain imaging (OFDI), a second-generation optical coherence tomography (OCT) technology, enables imaging of the three-dimensional (3D) microstructure of the vessel wall following a short and nonocclusive clear liquid flush. Although 3D vascular visualization provides a greater appreciation of the vessel wall and intraluminal structures, a longitudinal imaging pitch that is several times bigger than the optical imaging resolution of the system has limited true high-resolution 3D imaging, mainly due to the slow scanning speed of previous imaging catheters. Here, we demonstrate high frame-rate intravascular OFDI in vivo, acquiring images at a rate of 350 frames per second. A custom-built, high-speed, and high-precision fiber-optic rotary junction provided uniform and high-speed beam scanning through a custom-made imaging catheter with an outer diameter of 0.87 mm. A 47-mm-long rabbit aorta was imaged in 3.7 seconds after a short contrast agent flush. The longitudinal imaging pitch was 34 μm, comparable to the transverse imaging resolution of the system. Three-dimensional volume-rendering showed greatly enhanced visualization of tissue microstructure and stent struts relative to what is provided by conventional intravascular imaging speeds.

High frame-rate intravascular optical frequency-domain imaging in vivo.

Balancing the amounts of enzymes is one of the important factors to achieve optimum performance of a designed metabolic pathway. However, the random mutagenesis approach is impractical since it requires searching an unnecessarily large number of variants and often results in searching a narrow range of expression levels which are out of optimal level. Here, we developed a predictive combinatorial design method, called UTR Library Designer, which systematically searches a large combinatorial space of expression levels. It accomplishes this by designing synthetic translation initiation region of mRNAs in a predictive way based on a thermodynamic model and genetic algorithm. Using this approach, we successfully enhanced lysine and hydrogen production in Escherichia coli. Our method significantly reduced the number of variants to be explored for covering large combinatorial space and efficiently enhanced pathway efficiency, thereby facilitating future efforts in metabolic engineering and synthetic biology.

Predictive combinatorial design of mRNA translation initiation regions for systematic optimization of gene expression levels.

Lipid-rich inflamed coronary plaques are prone to rupture. The purpose of this study was to assess lipid-rich inflamed plaques in vivo using fully integrated high-speed optical coherence tomography (OCT)/near-infrared fluorescence (NIRF) molecular imaging with a Food and Drug Administration-approved indocyanine green (ICG).

Fully integrated high-speed intravascular optical coherence tomography/near-infrared fluorescence structural/molecular imaging in vivo using a clinically available near-infrared fluorescence-emitting indocyanine green to detect inflamed lipid-rich atheromata in coronary-sized vessels.

We demonstrate a novel polarization-sensitive optical frequency domain imaging system employing passive polarization multiplexing. Simple modification of a fiber delay line in the wavelength-swept light source enables illumination with two perpendicular polarizations that are required for determination of the Stokes vector components of the light reflected from each depth of the tissue. This simple all-passive approach provides a robust and low-cost solution for PS imaging replacing relatively complex conventional schemes such as polarization modulation or frequency-encoded polarization multiplexing.

Polarization-sensitive OFDI using polarization-multiplexed wavelength-swept laser.

Frequency domain optical coherence tomography (FD-OCT) has become one of the important clinical tools for intracoronary imaging to diagnose and monitor coronary artery disease, which has been one of the leading causes of death. To help more accurate diagnosis and monitoring of the disease, many researchers have recently worked on visualization of various coronary microscopic features including stent struts by constructing three-dimensional (3D) volumetric rendering from series of cross-sectional intracoronary FD-OCT images. In this paper, we present the first, to our knowledge, "push-of-a-button" graphics processing unit (GPU)-accelerated framework for intracoronary OCT imaging. Our framework visualizes 3D microstructures of the vessel wall with stent struts from raw binary OCT data acquired by the system digitizer as one seamless process. The framework reports the state-of-the-art performance; from raw OCT data, it takes 4.7 seconds to provide 3D visualization of a 5-cm-long coronary artery (of size 1600 samples x 1024 A-lines x 260 frames) with stent struts and detection of malapposition automatically at the single push of a button.

GPU-accelerated framework for intracoronary optical coherence tomography imaging at the push of a button.

Inflammation plays essential role in development of plaque disruption and coronary stent-associated complications. This study aimed to examine whether intracoronary dual-modal optical coherence tomography (OCT)-near-infrared fluorescence (NIRF) structural-molecular imaging with indocyanine green (ICG) can estimate inflammation in swine coronary artery.

Intracoronary dual-modal optical coherence tomography-near-infrared fluorescence structural-molecular imaging with a clinical dose of indocyanine green for the assessment of high-risk plaques and stent-associated inflammation in a beating coronary artery.

Macrophages mediate atheroma expansion and disruption, and denote high-risk arterial plaques. Therefore, they are substantially gaining importance as a diagnostic imaging target for the detection of rupture-prone plaques. Here, we developed an injectable near-infrared fluorescence (NIRF) probe by chemically conjugating thiolated glycol chitosan with cholesteryl chloroformate, NIRF dye (cyanine 5.5 or 7), and maleimide-polyethylene glycol-mannose as mannose receptor binding ligands to specifically target a subset of macrophages abundant in high-risk plaques. This probe showed high affinity to mannose receptors, low toxicity, and allowed the direct visualization of plaque macrophages in murine carotid atheroma. After the scale-up of the MMR-NIRF probe, the administration of the probe facilitated in vivo intravascular imaging of plaque inflammation in coronary-sized vessels of atheromatous rabbits using a custom-built dual-modal optical coherence tomography (OCT)-NIRF catheter-based imaging system. This novel imaging approach represents a potential imaging strategy enabling the identification of high-risk plaques in vivo and holds promise for future clinical implications.

Intravascular optical imaging of high-risk plaques in vivo by targeting macrophage mannose receptors.

ECG-Triggered, Single Cardiac Cycle, High-Speed, 3D, Intracoronary OCT.

We present a synthetic gene circuit for decoupling cell growth from metabolite production through autonomous regulation of enzymatic pathways by integrated modules that sense nutrient and substrate. The two-layer circuit allows Escherichia coli to selectively utilize target substrates in a mixed pool; channel metabolic resources to growth by delaying enzymatic conversion until nutrient depletion; and activate, terminate, and re-activate conversion upon substrate availability. We developed two versions of controller, both of which have glucose nutrient sensors but differ in their substrate-sensing modules. One controller is specific for hydroxycinnamic acid and the other for oleic acid. Our hydroxycinnamic acid controller lowered metabolic stress 2-fold and increased the growth rate 2-fold and productivity 5-fold, whereas our oleic acid controller lowered metabolic stress 2-fold and increased the growth rate 1.3-fold and productivity 2.4-fold. These results demonstrate the potential for engineering strategies that decouple growth and production to make bio-based production more economical and sustainable.

Article	Year
Engineering the pentose phosphate pathway to improve hydrogen yield in recombinant Escherichia coli. Biotechnology and bioengineering\| PubMed ID: 21732330	2011
Engineering glyceraldehyde-3-phosphate dehydrogenase for switching control of glycolysis in Escherichia coli. Biotechnology and bioengineering\| PubMed ID: 22528318	2012
High frame-rate intravascular optical frequency-domain imaging in vivo. Biomedical optics express\| PubMed ID: 24466489	2013
Predictive combinatorial design of mRNA translation initiation regions for systematic optimization of gene expression levels. Scientific reports\| PubMed ID: 24682040	2014
Fully integrated high-speed intravascular optical coherence tomography/near-infrared fluorescence structural/molecular imaging in vivo using a clinically available near-infrared fluorescence... Circulation. Cardiovascular interventions\| PubMed ID: 25074255	2014
Polarization-sensitive OFDI using polarization-multiplexed wavelength-swept laser. Optics letters\| PubMed ID: 25121652	2014
GPU-accelerated framework for intracoronary optical coherence tomography imaging at the push of a button. PloS one\| PubMed ID: 25880375	2015
Intracoronary dual-modal optical coherence tomography-near-infrared fluorescence structural-molecular imaging with a clinical dose of indocyanine green for the assessment of high-risk plaque... European heart journal\| PubMed ID: 26787442	2016
Intravascular optical imaging of high-risk plaques in vivo by targeting macrophage mannose receptors. Scientific reports\| PubMed ID: 26948523	2016
ECG-Triggered, Single Cardiac Cycle, High-Speed, 3D, Intracoronary OCT. JACC. Cardiovascular imaging\| PubMed ID: 27151525	2016
A Two-Layer Gene Circuit for Decoupling Cell Growth from Metabolite Production. Cell systems\| PubMed ID: 27559924	2016

Han-Saem Cho

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