An overview on biofuel and biochemical production by photosynthetic microorganisms with understanding of the metabolism and by metabolic engineering together with efficient cultivation and downstream processing

Sarkar, D.; Shimizu, Kazuyuki

doi:10.1186/s40643-015-0045-9

Cited by 46 publications

(21 citation statements)

References 217 publications

(243 reference statements)

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“…It is believed that a minimal cell could have beneficial properties for industrial applications. E. coli strains without redundant metabolic pathways produced much higher quantities of ethanol from hexose and pentose sugars [35,36]. E. coli lacking 22% of the genomic DNA produced 2.4-fold more threonine than the wild-type strain did [37].…”

Section: Minimal Genome Prediction and Minimal Cell Factory Designmentioning

confidence: 99%

Reframed Genome-Scale Metabolic Model to Facilitate Genetic Design and Integration with Expression Data

Jian

Zhang

et al. 2017

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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Genome-scale metabolic network models (GEMs) have played important roles in the design of genetically engineered strains and helped biologists to decipher metabolism. However, due to the complex gene-reaction relationships that exist in model systems, most algorithms have limited capabilities with respect to directly predicting accurate genetic design for metabolic engineering. In particular, methods that predict reaction knockout strategies leading to overproduction are often impractical in terms of gene manipulations. Recently, we proposed a method named logical transformation of model (LTM) to simplify the gene-reaction associations by introducing intermediate pseudo reactions, which makes it possible to generate genetic design. Here, we propose an alternative method to relieve researchers from deciphering complex gene-reactions by adding pseudo gene controlling reactions. In comparison to LTM, this new method introduces fewer pseudo reactions and generates a much smaller model system named as gModel. We showed that gModel allows two seldom reported applications: identification of minimal genomes and design of minimal cell factories within a modified OptKnock framework. In addition, gModel could be used to integrate expression data directly and improve the performance of the E-Fmin method for predicting fluxes. In conclusion, the model transformation procedure will facilitate genetic research based on GEMs, extending their applications.

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Section: Minimal Genome Prediction and Minimal Cell Factory Designmentioning

confidence: 99%

Reframed Genome-Scale Metabolic Model to Facilitate Genetic Design and Integration with Expression Data

Jian

Zhang

et al. 2017

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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“…Potential solutions to this global challenge include the use of photosynthetic microorganisms to produce biomass and lipids. These microorganisms fix carbon dioxide, in the presence of light and nutrients, but are limited by productivity and volumetric yield [ 2 ]. Heterotrophic microorganisms present a nearer term solution to this biofuel challenge, efficiently converting fixed carbon into biomass and lipids, with productivities and yields that are commercially relevant.…”

Section: Introductionmentioning

confidence: 99%

Engineering xylose metabolism in thraustochytrid T18

Merkx-Jacques

Rasmussen

Muise

et al. 2018

Biotechnol Biofuels

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BackgroundThraustochytrids are heterotrophic, oleaginous, marine protists with a significant potential for biofuel production. High-value co-products can off-set production costs; however, the cost of raw materials, and in particular carbon, is a major challenge to developing an economical viable production process. The use of hemicellulosic carbon derived from agricultural waste, which is rich in xylose and glucose, has been proposed as a sustainable and low-cost approach. Thraustochytrid strain T18 is a commercialized environmental isolate that readily consumes glucose, attaining impressive biomass, and oil production levels. However, neither thraustochytrid growth capabilities in the presence of xylose nor a xylose metabolic pathway has been described. The aims of this study were to identify and characterize the xylose metabolism pathway of T18 and, through genetic engineering, develop a strain capable of growth on hemicellulosic sugars.ResultsCharacterization of T18 performance in glucose/xylose media revealed diauxic growth and copious extracellular xylitol production. Furthermore, T18 did not grow in media containing xylose as the only carbon source. We identified, cloned, and functionally characterized a xylose isomerase. Transcriptomics indicated that this xylose isomerase gene is upregulated when xylose is consumed by the cells. Over-expression of the native xylose isomerase in T18, creating strain XI 16, increased xylose consumption from 5.2 to 7.6 g/L and reduced extracellular xylitol from almost 100% to 68%. Xylose utilization efficiency of this strain was further enhanced by over-expressing a heterologous xylulose kinase to reduce extracellular xylitol to 20%. Moreover, the ability to grow in media containing xylose as a sole sugar was dependent on the copy number of both xylose isomerase and xylulose kinase present. In fed-batch fermentations, the best xylose metabolizing isolate, XI-XK 7, used 137 g of xylose versus 39 g by wild type and produced more biomass and fatty acid.ConclusionsThe presence of a typically prokaryotic xylose isomerase and xylitol production through a typically eukaryotic xylose reductase pathway in T18 is the first report of an organism naturally encoding enzymes from two native xylose metabolic pathways. Our newly engineered strains pave the way for the growth of T18 on waste hemicellulosic feedstocks for biofuel production.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1246-1) contains supplementary material, which is available to authorized users.

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“…Furthermore, systems biology and synthetic biology perspectives and approaches are emerging in the production of bioactive compounds, such as carotenoids and vitamins, in algae [6,7]. In addition, using in silico metabolic models to complement and contextualize genetic and metabolic data will provide researchers more options for the strain improvement of target products [8,9,10,11]. However, the progress in the field is not well documented, and significant achievements on developing algal cell factories are yet to be recognized.…”

Section: Introductionmentioning

confidence: 99%

Algal Cell Factories: Approaches, Applications, and Potentials

Fu¹,

Chaiboonchoe²,

Khraiwesh

et al. 2016

Marine Drugs

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With the advent of modern biotechnology, microorganisms from diverse lineages have been used to produce bio-based feedstocks and bioactive compounds. Many of these compounds are currently commodities of interest, in a variety of markets and their utility warrants investigation into improving their production through strain development. In this review, we address the issue of strain improvement in a group of organisms with strong potential to be productive “cell factories”: the photosynthetic microalgae. Microalgae are a diverse group of phytoplankton, involving polyphyletic lineage such as green algae and diatoms that are commonly used in the industry. The photosynthetic microalgae have been under intense investigation recently for their ability to produce commercial compounds using only light, CO2, and basic nutrients. However, their strain improvement is still a relatively recent area of work that is under development. Importantly, it is only through appropriate engineering methods that we may see the full biotechnological potential of microalgae come to fruition. Thus, in this review, we address past and present endeavors towards the aim of creating productive algal cell factories and describe possible advantageous future directions for the field.

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An overview on biofuel and biochemical production by photosynthetic microorganisms with understanding of the metabolism and by metabolic engineering together with efficient cultivation and downstream processing

Cited by 46 publications

References 217 publications

Reframed Genome-Scale Metabolic Model to Facilitate Genetic Design and Integration with Expression Data

Reframed Genome-Scale Metabolic Model to Facilitate Genetic Design and Integration with Expression Data

Engineering xylose metabolism in thraustochytrid T18

Algal Cell Factories: Approaches, Applications, and Potentials

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