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Chassis optimization as a cornerstone for the application of synthetic biology based strategies in microbial secondary metabolism.

Beites T, Mendes MV - Front Microbiol (2015)

Bottom Line: Activation of the biosynthetic gene clusters that present reduced or no expression (known as cryptic or silent clusters) by heterologous expression has emerged as a strategy for the identification and production of novel bioactive molecules.In this review we present an overview on the strategies and tools used in the development of hosts/chassis for the heterologous expression of specialized metabolites biosynthetic gene clusters.Finally, we introduce the concept of specialized host as the next step of development of expression hosts.

View Article: PubMed Central - PubMed

Affiliation: I3S Instituto de Investigação e Inovação em Saúde, Universidade do Porto Porto, Portugal ; Instituto de Biologia Molecular e Celular, Universidade do Porto Porto, Portugal.

ABSTRACT
The increased number of bacterial genome sequencing projects has generated over the last years a large reservoir of genomic information. In silico analysis of this genomic data has renewed the interest in bacterial bioprospecting for bioactive compounds by unveiling novel biosynthetic gene clusters of unknown or uncharacterized metabolites. However, only a small fraction of those metabolites is produced under laboratory-controlled conditions; the remaining clusters represent a pool of novel metabolites that are waiting to be "awaken". Activation of the biosynthetic gene clusters that present reduced or no expression (known as cryptic or silent clusters) by heterologous expression has emerged as a strategy for the identification and production of novel bioactive molecules. Synthetic biology, with engineering principles at its core, provides an excellent framework for the development of efficient heterologous systems for the expression of biosynthetic gene clusters. However, a common problem in its application is the host-interference problem, i.e., the unpredictable interactions between the device and the host that can hamper the desired output. Although an effort has been made to develop orthogonal devices, the most proficient way to overcome the host-interference problem is through genome simplification. In this review we present an overview on the strategies and tools used in the development of hosts/chassis for the heterologous expression of specialized metabolites biosynthetic gene clusters. Finally, we introduce the concept of specialized host as the next step of development of expression hosts.

No MeSH data available.


Related in: MedlinePlus

Optimized workflow for the heterologous expression of biosynthetic gene clusters. Applying the concept of genome simplification, one should expect that the host-interference problem would be minimized rendering more efficient strains. The methods of gene delivery and cluster refactoring can also improve the desired outcome, i.e., strains combining the ability to produce heterologous cryptic compounds and to behave as over-producers.
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Figure 1: Optimized workflow for the heterologous expression of biosynthetic gene clusters. Applying the concept of genome simplification, one should expect that the host-interference problem would be minimized rendering more efficient strains. The methods of gene delivery and cluster refactoring can also improve the desired outcome, i.e., strains combining the ability to produce heterologous cryptic compounds and to behave as over-producers.

Mentions: From a biotechnological point of view, top–down strategies are the most attractive, because they consist in the reduction of existing genomes. By deleting parts that are predicted to be non-essential to the microorganisms, or parts that may contribute negatively to the pretended outcome, it is expected to obtain more efficient and tractable chassis. Indeed, genome reduction by the deletion of non-essential genes has resulted in increased genome stability, growth robustness, simplification of the secreted metabolome and increased availability of precursor units (Gomez-Escribano and Bibb, 2011; Zhou et al., 2012; Komatsu et al., 2013). Genome reduction as the first step in the heterologous expression workflow is expected to render strains that will not only be capable of producing cryptic specialized metabolites, but also to over-produce the final product (Figure 1).


Chassis optimization as a cornerstone for the application of synthetic biology based strategies in microbial secondary metabolism.

Beites T, Mendes MV - Front Microbiol (2015)

Optimized workflow for the heterologous expression of biosynthetic gene clusters. Applying the concept of genome simplification, one should expect that the host-interference problem would be minimized rendering more efficient strains. The methods of gene delivery and cluster refactoring can also improve the desired outcome, i.e., strains combining the ability to produce heterologous cryptic compounds and to behave as over-producers.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4563238&req=5

Figure 1: Optimized workflow for the heterologous expression of biosynthetic gene clusters. Applying the concept of genome simplification, one should expect that the host-interference problem would be minimized rendering more efficient strains. The methods of gene delivery and cluster refactoring can also improve the desired outcome, i.e., strains combining the ability to produce heterologous cryptic compounds and to behave as over-producers.
Mentions: From a biotechnological point of view, top–down strategies are the most attractive, because they consist in the reduction of existing genomes. By deleting parts that are predicted to be non-essential to the microorganisms, or parts that may contribute negatively to the pretended outcome, it is expected to obtain more efficient and tractable chassis. Indeed, genome reduction by the deletion of non-essential genes has resulted in increased genome stability, growth robustness, simplification of the secreted metabolome and increased availability of precursor units (Gomez-Escribano and Bibb, 2011; Zhou et al., 2012; Komatsu et al., 2013). Genome reduction as the first step in the heterologous expression workflow is expected to render strains that will not only be capable of producing cryptic specialized metabolites, but also to over-produce the final product (Figure 1).

Bottom Line: Activation of the biosynthetic gene clusters that present reduced or no expression (known as cryptic or silent clusters) by heterologous expression has emerged as a strategy for the identification and production of novel bioactive molecules.In this review we present an overview on the strategies and tools used in the development of hosts/chassis for the heterologous expression of specialized metabolites biosynthetic gene clusters.Finally, we introduce the concept of specialized host as the next step of development of expression hosts.

View Article: PubMed Central - PubMed

Affiliation: I3S Instituto de Investigação e Inovação em Saúde, Universidade do Porto Porto, Portugal ; Instituto de Biologia Molecular e Celular, Universidade do Porto Porto, Portugal.

ABSTRACT
The increased number of bacterial genome sequencing projects has generated over the last years a large reservoir of genomic information. In silico analysis of this genomic data has renewed the interest in bacterial bioprospecting for bioactive compounds by unveiling novel biosynthetic gene clusters of unknown or uncharacterized metabolites. However, only a small fraction of those metabolites is produced under laboratory-controlled conditions; the remaining clusters represent a pool of novel metabolites that are waiting to be "awaken". Activation of the biosynthetic gene clusters that present reduced or no expression (known as cryptic or silent clusters) by heterologous expression has emerged as a strategy for the identification and production of novel bioactive molecules. Synthetic biology, with engineering principles at its core, provides an excellent framework for the development of efficient heterologous systems for the expression of biosynthetic gene clusters. However, a common problem in its application is the host-interference problem, i.e., the unpredictable interactions between the device and the host that can hamper the desired output. Although an effort has been made to develop orthogonal devices, the most proficient way to overcome the host-interference problem is through genome simplification. In this review we present an overview on the strategies and tools used in the development of hosts/chassis for the heterologous expression of specialized metabolites biosynthetic gene clusters. Finally, we introduce the concept of specialized host as the next step of development of expression hosts.

No MeSH data available.


Related in: MedlinePlus