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      Engineering the methylerythritol phosphate pathway in cyanobacteria for photosynthetic isoprene production from CO2

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          Abstract

          The methylerythritol phosphate pathway in photosynthetic cyanobacteria was engineered to allow highly efficient production of isoprene from CO 2.

          Isoprene, a key building block of synthetic rubber, is currently produced entirely from petrochemical sources. Previous metabolic engineering efforts, centered on heterologous expression of the mevalonate pathway, have resulted in isoprene production by microbial fermentation of sugars. To produce isoprene directly from CO 2, we engineered the isoprene biosynthetic pathway in the cyanobacterium Synechococcus elongatus, with guidance provided by dynamic flux analysis and metabolite profiling. The methylerythritol phosphate (MEP) pathway was selected for cyanobacterial isoprene synthesis based on comparison of carbon efficiency and the precursor driving force between the MEP pathway and the mevalonate pathway. Plant-derived isoprene synthases with high activities were introduced, followed by increasing the ratio of dimethylallyl pyrophosphate to isopentenyl pyrophosphate (IPP) by overexpression of IPP isomerase (IDI), further improvement in isoprene production activity by direct fusion of IDI and isoprene synthase, and relieving an MEP pathway bottleneck identified by kinetic flux profiling. The engineered strain directed about 40% of photosynthetically fixed carbon toward the isoprene biosynthetic pathway, resulting in the production of 1.26 g L −1 of isoprene from CO 2, which is a significant increase for terpenoid production by photoautotrophic microorganisms. The strains developed in this study can serve as platform hosts for photosynthetic production of diverse terpenoids from CO 2.

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          A positive/negative ion-switching, targeted mass spectrometry-based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue.

          The revival of interest in cancer cell metabolism in recent years has prompted the need for quantitative analytical platforms for studying metabolites from in vivo sources. We implemented a quantitative polar metabolomics profiling platform using selected reaction monitoring with a 5500 QTRAP hybrid triple quadrupole mass spectrometer that covers all major metabolic pathways. The platform uses hydrophilic interaction liquid chromatography with positive/negative ion switching to analyze 258 metabolites (289 Q1/Q3 transitions) from a single 15-min liquid chromatography-mass spectrometry acquisition with a 3-ms dwell time and a 1.55-s duty cycle time. Previous platforms use more than one experiment to profile this number of metabolites from different ionization modes. The platform is compatible with polar metabolites from any biological source, including fresh tissues, cancer cells, bodily fluids and formalin-fixed paraffin-embedded tumor tissue. Relative quantification can be achieved without using internal standards, and integrated peak areas based on total ion current can be used for statistical analyses and pathway analyses across biological sample conditions. The procedure takes ∼12 h from metabolite extraction to peak integration for a data set containing 15 total samples (∼6 h for a single sample).
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            Isoprenoid biosynthesis: the evolution of two ancient and distinct pathways across genomes.

            Isopentenyl diphosphate (IPP) is the central intermediate in the biosynthesis of isoprenoids, the most ancient and diverse class of natural products. Two distinct routes of IPP biosynthesis occur in nature: the mevalonate pathway and the recently discovered deoxyxylulose 5-phosphate (DXP) pathway. The evolutionary history of the enzymes involved in both routes and the phylogenetic distribution of their genes across genomes suggest that the mevalonate pathway is germane to archaebacteria, that the DXP pathway is germane to eubacteria, and that eukaryotes have inherited their genes for IPP biosynthesis from prokaryotes. The occurrence of genes specific to the DXP pathway is restricted to plastid-bearing eukaryotes, indicating that these genes were acquired from the cyanobacterial ancestor of plastids. However, the individual phylogenies of these genes, with only one exception, do not provide evidence for a specific affinity between the plant genes and their cyanobacterial homologues. The results suggest that lateral gene transfer between eubacteria subsequent to the origin of plastids has played a major role in the evolution of this pathway.
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              Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized.

              The cornerstone of autotrophy, the CO(2)-fixing enzyme, d-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), is hamstrung by slow catalysis and confusion between CO(2) and O(2) as substrates, an "abominably perplexing" puzzle, in Darwin's parlance. Here we argue that these characteristics stem from difficulty in binding the featureless CO(2) molecule, which forces specificity for the gaseous substrate to be determined largely or completely in the transition state. We hypothesize that natural selection for greater CO(2)/O(2) specificity, in response to reducing atmospheric CO(2):O(2) ratios, has resulted in a transition state for CO(2) addition in which the CO(2) moiety closely resembles a carboxylate group. This maximizes the structural difference between the transition states for carboxylation and the competing oxygenation, allowing better differentiation between them. However, increasing structural similarity between the carboxylation transition state and its carboxyketone product exposes the carboxyketone to the strong binding required to stabilize the transition state and causes the carboxyketone intermediate to bind so tightly that its cleavage to products is slowed. We assert that all Rubiscos may be nearly perfectly adapted to the differing CO(2), O(2), and thermal conditions in their subcellular environments, optimizing this compromise between CO(2)/O(2) specificity and the maximum rate of catalytic turnover. Our hypothesis explains the feeble rate enhancement displayed by Rubisco in processing the exogenously supplied carboxyketone intermediate, compared with its nonenzymatic hydrolysis, and the positive correlation between CO(2)/O(2) specificity and (12)C/(13)C fractionation. It further predicts that, because a more product-like transition state is more ordered (decreased entropy), the effectiveness of this strategy will deteriorate with increasing temperature.
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                Author and article information

                Journal
                EESNBY
                Energy & Environmental Science
                Energy Environ. Sci.
                Royal Society of Chemistry (RSC)
                1754-5692
                1754-5706
                2016
                2016
                : 9
                : 4
                : 1400-1411
                Article
                10.1039/C5EE03102H
                f27e80a2-a03a-4e68-852e-c261bee884c2
                © 2016
                History

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