Evaluating Factors That Influence Microbial Synthesis Yields by Linear Regression with Numerical and Ordinal Variables

Colletti, Peter; Goyal, Yogesh; Varman, Arul M.; Feng, Xueyang; Wu, Bing; Tang, Yinjie J.

doi:10.1002/bit.22996

Cited by 31 publications

(23 citation statements)

References 42 publications

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“…Among the next-generation biofuels synthesized from pyruvate, IB possesses fewer reaction steps (5 reaction steps from pyruvate to IB) than the synthesis of 1-butanol or biodiesel. IB is less toxic to microbes (5), so it may achieve a higher product titer and yield (6,7). For example, a maximum titer of 50.8 g/liter of IB can be achieved in an engineered Escherichia coli strain (8).…”

mentioning

confidence: 99%

Metabolic Engineering of Synechocystis sp. Strain PCC 6803 for Isobutanol Production

Varman¹,

Xiao²,

Pakrasi

et al. 2013

Appl Environ Microbiol

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156

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Global warming and decreasing fossil fuel reserves have prompted great interest in the synthesis of advanced biofuels from renewable resources. In an effort to address these concerns, we performed metabolic engineering of the cyanobacterium Synechocystis sp. strain PCC 6803 to develop a strain that can synthesize isobutanol under both autotrophic and mixotrophic conditions. With the expression of two heterologous genes from the Ehrlich pathway, the engineered strain can accumulate 90 mg/ liter of isobutanol from 50 mM bicarbonate in a gas-tight shaking flask. The strain does not require any inducer (i.e., isopropyl ␤-D-1-thiogalactopyranoside [IPTG]) or antibiotics to maintain its isobutanol production. In the presence of glucose, isobutanol synthesis is only moderately promoted (titer ‫؍‬ 114 mg/liter). Based on isotopomer analysis, we found that, compared to the wild-type strain, the mutant significantly reduced its glucose utilization and mainly employed autotrophic metabolism for biomass growth and isobutanol production. Since isobutanol is toxic to the cells and may also be degraded photochemically by hydroxyl radicals during the cultivation process, we employed in situ removal of the isobutanol using oleyl alcohol as a solvent trap. This resulted in a final net concentration of 298 mg/liter of isobutanol under mixotrophic culture conditions. G lobal energy needs continue to increase rapidly due to industrial and development demands, raising environmental concerns. Much of the worldwide energy consumption comes from the burning of fossil fuels, which produces about 6 gigatons of CO 2 annually (1). Increasing CO 2 levels may act as a feedback loop to increase the soil emissions of other greenhouse gases, such as methane and nitrous oxide, raising the global temperature (2). For energy security and due to environmental concerns, there is an urgent demand for the development of bioenergy. Bioethanol is the most common biofuel, but it also has low energy density and absorbs moisture. Isobutanol (IB) is a better fuel, because it is less water soluble and has an energy density/octane value close to that of gasoline (3, 4). Among the next-generation biofuels synthesized from pyruvate, IB possesses fewer reaction steps (5 reaction steps from pyruvate to IB) than the synthesis of 1-butanol or biodiesel. IB is less toxic to microbes (5), so it may achieve a higher product titer and yield (6, 7). For example, a maximum titer of 50.8 g/liter of IB can be achieved in an engineered Escherichia coli strain (8).On the other hand, cyanobacteria not only can convert CO 2 into bioproducts, but also can play an important role in environmental bioremediation. The photosynthetic efficiency of cyanobacteria (3 to 9%) is high compared to that of higher plants (Յ0.25 to 3%) (9, 10). Furthermore, some species of cyanobacteria are amenable to genetic engineering. Table 1 lists the various biofuels that have been synthesized through the metabolic engineering of cyanobacteria. Autotrophic IB production in cyanobacteria was first demons...

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mentioning

confidence: 99%

Metabolic Engineering of Synechocystis sp. Strain PCC 6803 for Isobutanol Production

Varman¹,

Xiao²,

Pakrasi

et al. 2013

Appl Environ Microbiol

Self Cite

156

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“…Although these metabolic engineering strategies are effective in increasing the carbon flux toward the desired product, metabolic engineers cannot easily create “biofuel super bugs”. Extensive genetic modifications often increase metabolic burdens on the host and thus further interfere with cell growth and product synthesis (Colletti et al, 2011; Poust et al, 2014). For example, high copy number plasmids or strong promoter can place a heavy burden on the cell's growth and negatively affect productivity (Carrier et al, 1998; Jones et al, 2000).…”

Section: Metabolic Engineering Approaches For Biofuel Synthesismentioning

confidence: 99%

Biofuel production: an odyssey from metabolic engineering to fermentation scale-up

Hollinshead

Tang

2014

Front. Microbiol.

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Metabolic engineering has developed microbial cell factories that can convert renewable carbon sources into biofuels. Current molecular biology tools can efficiently alter enzyme levels to redirect carbon fluxes toward biofuel production, but low product yield and titer in large bioreactors prevent the fulfillment of cheap biofuels. There are three major roadblocks preventing economical biofuel production. First, carbon fluxes from the substrate dissipate into a complex metabolic network. Besides the desired product, microbial hosts direct carbon flux to synthesize biomass, overflow metabolites, and heterologous enzymes. Second, microbial hosts need to oxidize a large portion of the substrate to generate both ATP and NAD(P)H to power biofuel synthesis. High cell maintenance, triggered by the metabolic burdens from genetic modifications, can significantly affect the ATP supply. Thereby, fermentation of advanced biofuels (such as biodiesel and hydrocarbons) often requires aerobic respiration to resolve the ATP shortage. Third, mass transfer limitations in large bioreactors create heterogeneous growth conditions and micro-environmental fluctuations (such as suboptimal O2 level and pH) that induce metabolic stresses and genetic instability. To overcome these limitations, fermentation engineering should merge with systems metabolic engineering. Modern fermentation engineers need to adopt new metabolic flux analysis tools that integrate kinetics, hydrodynamics, and 13C-proteomics, to reveal the dynamic physiologies of the microbial host under large bioreactor conditions. Based on metabolic analyses, fermentation engineers may employ rational pathway modifications, synthetic biology circuits, and bioreactor control algorithms to optimize large-scale biofuel production.

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“…Systems biology knowledge will also make synthetic biology tools more reliable, enabling the precise control of transcription and translation regardless of the under-controlled gene (Mutalik et al, 2013). More powerful systems biology-based computational tools will simplify both the design and the optimization of synthetic metabolic pathways, improving titers and productivities (Colletti et al, 2011). Similarly, simplified genetic systems created in synthetic biology will provide systems biology with insight into the fundamentals of native gene regulation.…”

Section: Conclusion and Outlooksmentioning

confidence: 99%

Bridging the gap between systems biology and synthetic biology

Liu¹,

Hoynes-O’Connor²,

Zhang³

2013

Front. Microbiol.

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Systems biology is an inter-disciplinary science that studies the complex interactions and the collective behavior of a cell or an organism. Synthetic biology, as a technological subject, combines biological science and engineering, allowing the design and manipulation of a system for certain applications. Both systems and synthetic biology have played important roles in the recent development of microbial platforms for energy, materials, and environmental applications. More importantly, systems biology provides the knowledge necessary for the development of synthetic biology tools, which in turn facilitates the manipulation and understanding of complex biological systems. Thus, the combination of systems and synthetic biology has huge potential for studying and engineering microbes, especially to perform advanced tasks, such as producing biofuels. Although there have been very few studies in integrating systems and synthetic biology, existing examples have demonstrated great power in extending microbiological capabilities. This review focuses on recent efforts in microbiological genomics, transcriptomics, proteomics, and metabolomics, aiming to fill the gap between systems and synthetic biology.

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Evaluating Factors That Influence Microbial Synthesis Yields by Linear Regression with Numerical and Ordinal Variables

Cited by 31 publications

References 42 publications

Metabolic Engineering of Synechocystis sp. Strain PCC 6803 for Isobutanol Production

Metabolic Engineering of Synechocystis sp. Strain PCC 6803 for Isobutanol Production

Biofuel production: an odyssey from metabolic engineering to fermentation scale-up

Bridging the gap between systems biology and synthetic biology

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