Papers of the month – March

Welcome to our pick of papers and articles from the last month. These are a collection of the synthetic biology papers that have captured our attention and that we think you should know about. Maybe you’ve seen some others you’d like to tell us about. Send us a comment or tweet us at @synbiobydesign. See our previous recommended papers here.

 

Other notable published works includes: Roboliq: a software system for lab automation, a review of plant plastid and nuclear genome editing, a book on synthetic bioarchitectures, a review of synthetic biology applications to engineering the human microbiota, a review of circuit engineering for understanding basic biology, a review of advances in the Test component of the Design-Build-Test cycle in metabolomics, a review of the safety and security challenges that need to be addressed in Synbio, a review of bottom-up approaches for tissue engineering, a review of engineering microbial communities.

DNA parts & toolkits

Hybrid yeast promoters for inducible differential gene expression

Pothoulakis & Ellis have expanded the yeast promoter toolbox by engineering hybrid promoters from enhancer and core regions for yeast which are ATc-inducible specifically in haploid mother cells.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0194588

Constant gene expression regardless of copy number via control engineering

Gene expression of cloned genes is usually highly dependent on plasmid copy number and genome location. In this project, Segall-Shapiro et al. used a control theory approach to engineer independence of gene expression from these two factors. The addition of an incoherent feedforward loop (iFFL) counteracts the effect of copy number on the gene of interest and provides perfect adaptation. TALEs provided the necessary repression of the iFFL.

https://www.nature.com/articles/nbt.4111

Diagram of the incoherent feedforward loop from Segar-Shapiro et al., 2018.

Controlling burden

Addition and maintenance of synthetic circuitry places a burden on the cell as resources are redirected to expressing recombinant protein. In this work, the htpG1 promoter was identified as a good candidate for a burden biosensor, and also used in the design of a negative feedback controller. The htpG1 promoter was also used to drive the expression of a dead Cas9, which then repressed the synthetic constructs and reduced the burden.

https://www.nature.com/articles/nmeth.4635

A diagram of the circuit design by Ceroni et al. for a burden-based biomolecular control system

Systems and synthetic biology computational standards

This special issue of the Journal of Integrative Bioinformatics summarises the improvements of existing standards and novel standards from 2017, including SBOL (Synthetic Biology Open Language) and SBML (Systems Biology Markup Language). These all fall under the COMBINE (‘COmputational Modeling in BIology’ NEtwork) centralised platform.

https://www.degruyter.com/view/j/jib.ahead-of-print/jib-2018-0013/jib-2018-0013.xml

DNA assembly in plants

This review summarises the advances made in plant synthetic biology with regards to genetic engineering and genome editing, including DNA cloning and assembly such as BioBricks and Golden Gate, and standard toolkits and parts such as MoClo and GoldenBraid.

https://www.sciencedirect.com/science/article/pii/S0168945217312062

CRISPR-CasX

Fine tuning gene expression using dCas9

A tunable repressor of E. coli genes was made by varying the levels of complementarity of the gRNA to the target. Catalytically dead Cas9 enzyme, dCas9, is used to bind DNA and act as a roadblock to RNA polymerase. It was shown that varying the number of mismatches at the 5’ end of the PAM determines repression strength and is favoured over tuning expression by changing the amount of dCas9.

http://msb.embopress.org/content/14/3/e7899

CRISPR for treating heart disease

This Nature Outlook article summarises the advances made in tackling cardiovascular disease using gene editing technology for vaccination. Some of the applications include reducing LDL cholesterol by disrupting the PCSK9 or ANGPTL3 enzyme or reducing the risk of cardiovascular disease by targeting the lipoprotein(a) gene.

https://www.nature.com/articles/d41586-018-02482-4

Microfluidics

Microfluidics platform for detecting recombinant protein expression

An automated induction microfluidic systems (AIMS) has been designed for strain engineering – screening strains for desired expression levels of proteins from synthetic circuitry. This is necessary due to the unexpected interactions between DNA parts and assay conditions. AIMS allows part characterisation and parameter optimisation for a low cost and with minimal intervention – growing the culture to optimal OD levels, induction and measuring recombinant protein levels are all done on the chip.

https://pubs.acs.org/doi/full/10.1021/acssynbio.8b00025

The AIMS platform for culturing cells, monitoring and controlling OD values and performing assays designed by Husser et al.

Microfluidics platforms for cell-free designs

This review summarises the state of the art of manipulating synthetic biological machinery within microfluidic chips. There is a large focus on in vitro protein synthesis, where the toxicity of the product, crosstalk from endogenous pathways, cloning difficulties and low yield make in vivo solutions inferior. Microfluidics platforms allow gene and protein synthesis to be automated (precise), cheap (less reagents needed), rapid and performed in a high throughput manner.

http://www.mdpi.com/2073-4425/9/3/144

Chassis

Microalgae for synbio

Nannochloropsis are a kind of microalgae that have been used in diverse biotechnology applications, including biofuel production due to its high oil content. This review summarises the available genomic data, transformation protocols and various studies performed in Nannochloropsis – vital information for establishing as a chassis for synbio.

https://link.springer.com/article/10.1007%2Fs00299-018-2270-0

Leave a Reply

Your email address will not be published. Required fields are marked *