Session 7

Khou et al., (2015) Distributing a metabolic pathway among a microbial consortium enhances production of natural products

Key findings:
The aim of the group of Stephanopoulos is to reconstruct a heterologous pathway for a paclitaxel precursor in a microbial partnership.
Therefore, one microbe (E. coli) is engineered to synthesize a metabolic intermediate (taxadiene) which is functionalized by another microbe (S. cerevisiae) producing an activated form of a precursors of the anti-cancer drug paclitaxel. Neither E. coli nor S. cerevisiae can produce the paclitaxel precursor itself. To overcome an inhibition of E. coli by the ethanol S. cerevisiae produced while growing on glucose, a mutualistic interaction between the two microorganisms was created. The co-culture carbon source was switched from glucose to xylose which was used by E. coli and metabolized to acetate which further served as carbon source for S. cerevisiae. By increasing the initial inoculum of yeast and periodically feeding additional xylose, ammonium, and phosphorus, a limitation of nutrients as well as an accumulation of acetate could be eliminated. The taxadiene oxygenation efficiency by S. cerevisiae was further improved by exchanging the TEF promoter by a UAS-GPD promoter.

Relevance of the article:
High relevance: The titers of isoprenoids produced with the methods described above are higher than reported previously. Furthermore, the strategies are widely applicable: the researchers used a co-cultivation of the previously described organisms to produce different oxygenated isoprenoids like Nootkatone and Ferruginol.

Rating (‘Exceptional – a must read paper’, ‘Very good – worth spending the time’, ‘Good – only if you have time to spare’).
Exceptional

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Session 6

Leber at al., (2013). Engineering of Saccharomyces cerevisiae for the Synthesis of Short Chain Fatty Acids.

Key findings:

The introduction of human Fatty acid synthase (FAS) and exogenous short chain thioesterases in S. cerevisiae increased in vivo caprylic acid (octanoic acid) and total SCFA production up to 64-fold (63 mg/L) and 52-fold (68mg/L). Combined over-expression of the phosphopantetheine transferase (PPT) with the human FAS mutant resulted in octanoic acid titers of up to 82 mg/L and total SCFA titers of up to 111 mg/L. No significant improves were shown in the production of caproic acid (hexanoic acid).

In this publication it was also demonstrated the functional replacement of the native fungal FAS by human FAS, an experiment in which human FAS was overexpressed in a FAS2 knockout strain (deficient in de novo fatty acid synthesis).

Relevance of the article:

This is the first report of an active mammalian FAS expressed in yeast and the first report of the in vivoproduction of SCFAs in S. cerevisiae.

S. cerevisiae.was engineered to produce SCFAs by introducing the human FAS and heterologous short chain thioesterases genes. Exogenous phosphopantetheine transfereases (PPTs) were expressed to create the active holo-hFAS form, and in vitro and in vivo activity of the hFAS was confirmed. The thioesterase domain was removed from hFAS to allow the premature cleaving of the elongating fatty acids by independent or linked exogeneous short chain TEs and the production of SCFAs was demonstrated.

Rating (‘Exceptional – a must read paper’, ‘Very good – worth spending the time’, ‘Good – only if you have time to spare’).

Very good paper.

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Session 5

Marie-Nelly et al., (2014). High-quality genome (re)assembly using chromosomal contact data

Key findings:

The authors of this article presented a new algorithm to assemble genome sequences. This software, called GRAAL, makes use of the reads obtained by the sequencing platforms and also considers structural information obtained from 3C and Hi-C experimental methods. Continue reading

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Session 4

Matsuo et al., (2013). Coupled GTPase and remodelling ATPase activities form a checkpoint for ribosome export.

Key findings:

Protein biosynthesis is a very complicated, multistage process subjected to strict control. The genetic information has to be very carefully read and rewritten. The translation step involves ribosomes, RNA and many proteins, and its regulation begins in the nucleus. Continue reading

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Session 3

Luque et al., (2014) In vivo evolution of metabolic pathways by homeologous recombination in mitotic cells.

So far, engineering of metabolic pathways has relied on in vitro techniques that can lead to the production of better enzymes, for example with more substrate specificity or better kinetic properties. Continue reading

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Session 2

Zid et al., (2014) Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast.

Key findings:

The authors used novel approach, ribosome profiling, to identify upregulated mRNAs during yeast starvation. Also they have found that those mRNAs have different translation activity directed by promoter sequence. Continue reading

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Session 1

Fischer et al. (2011), Metabolic Engineering of Monoterpene Synthesis in Yeast, Biotechnology and Bioengineering.

Key findings:
Wild S. cerevisiae strains are – with a few exceptions for winemaking strains up to 5 µg/L – not able to produce monoterpenes. Unlike plants microorganisms usually do not carry a specific geranyl diphosphate (GPP) synthetase. Continue reading

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Evolution of metabolic pathways

by Manuela Gottardi.

Thanks to developments in biotechnology it is possible nowadays to produce chemicals through biological ways, therefore avoiding the use of non-renewable sources, such as petroleum. In order to produce compounds through biological processes, microorganisms have been modified and engineered. Continue reading

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Yeast hybridization: a solution for biodiversity conservation?

by Frederico Magalhães.

For thousands of years humans have been intuitively selecting plants or animals to crossbreed in order to improve the traits of the crops or livestock. A similar situation must have occurred with the yeast lineages associated with fermented beverages. Its close association with human activities has led to the so-called domestication of these species, resulting in industrial strains that perform remarkably well in each specific application, but whose performance may be severely reduced in a different environment (Steensels et al., 2014). The hybridization of yeast strains is one of the most important mechanisms leading to the generation of strains with improved properties and increasing the genetic diversity of yeasts. Continue reading

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How to get several genes simultaneously integrated into the genome of Saccharomyces cerevisiae?

by Leonie Wenning.

Probably everybody in the 21st century has already heard the term “genetically modified organism” (GMO). Many people who hear this term think of something artificial or/and negative. But in fact, the basics of many methods which are used today to specifically modify organisms have been developed by the organisms themselves during evolution of the species. Continue reading

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