Bridging Omics Technologies with Synthetic Biology in Yeast Industrial Biotechnology

Despite the availability of a variety of ' -omics ' technologies to support the system-wide analysis of industrially relevant microorganisms, the manipulation of strains towards an economically relevant goal remains a challenge. Remarkably, our ability to catalogue the participants in and model ever more comprehensive aspects of a microorganism's physiology is now complemented by technologies that permanently expand the scope of engineering interventions that can be imagined. In fact, genome-wide editing and re-synthesis of microbial and even eukaryotic chromosomes have become widely applied methods. At the heart of this emerging system-wide engineering approach, often labelled ' Synthetic Biology ' , is the continuous improvement of large-scale DNA synthesis, which is put to two-fold use: (i) starting ever more ambitious efforts to re-write existing and coding novel molecular systems, and (ii) designing and constructing increasingly sophisticated library technologies, which has led to a renaissance of directed evolution in strain engineering. Here, we briefly review some of the critical concepts and technological stepping-stones of Synthetic Biology on its way to becoming a mature industrial technology.

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Synthetic biology biosensors for healthcare and industrial biotechnology applications

IET/SynbiCITE Engineering Biology Conference ◽

10.1049/cp.2016.1235 ◽

2016 ◽

Author(s):

K.M. Polizzi ◽

P.S. Freemont

Keyword(s):

Synthetic Biology ◽

Industrial Biotechnology

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Halomonas as a chassis

Essays in Biochemistry ◽

10.1042/ebc20200159 ◽

2021 ◽

Author(s):

Jian-Wen Ye ◽

Guo-Qiang Chen

Keyword(s):

Synthetic Biology ◽

Rapid Development ◽

High Energy ◽

Strain Engineering ◽

Current Status ◽

Industrial Biotechnology ◽

Cell Factories ◽

Energy Consuming ◽

Significant Cost Reduction ◽

Process Complexity

Abstract With the rapid development of systems and synthetic biology, the non-model bacteria, Halomonas spp., have been developed recently to become a cost-competitive platform for producing a variety of products including polyesters, chemicals and proteins owing to their contamination resistance and ability of high cell density growth at alkaline pH and high salt concentration. These salt-loving microbes can partially solve the challenges of current industrial biotechnology (CIB) which requires high energy-consuming sterilization to prevent contamination as CIB is based on traditional chassis, typically, Escherichia coli, Bacillus subtilis, Pseudomonas putida and Corynebacterium glutamicum. The advantages and current status of Halomonas spp. including their molecular biology and metabolic engineering approaches as well as their applications are reviewed here. Moreover, a systematic strain engineering streamline, including product-based host development, genetic parts mining, static and dynamic optimization of modularized pathways and bioprocess-inspired cell engineering are summarized. All of these developments result in the term called next-generation industrial biotechnology (NGIB). Increasing efforts are made to develop their versatile cell factories powered by synthetic biology to demonstrate a new biomanufacturing strategy under open and continuous processes with significant cost-reduction on process complexity, energy, substrates and fresh water consumption.

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RetroPath2.0: a retrosynthesis workflow for metabolic engineers

10.1101/141721 ◽

2017 ◽

Cited By ~ 2

Author(s):

Baudoin Delépine ◽

Thomas Duigou ◽

Pablo Carbonell ◽

Jean-Loup Faulon

Keyword(s):

Synthetic Biology ◽

Open Source ◽

Computer Aided Design ◽

Reaction Network ◽

Ease Of Use ◽

Chemical Diversity ◽

Industrial Biotechnology ◽

List Type ◽

Enzyme Promiscuity ◽

Main Challenge

AbstractSynthetic biology applied to industrial biotechnology is transforming the way we produce chemicals. However, despite advances in the scale and scope of metabolic engineering, the bioproduction process still remains costly. In order to expand the chemical repertoire for the production of next generation compounds, a major engineering biology effort is required in the development of novel design tools that target chemical diversity through rapid and predictable protocols. Addressing that goal involves retrosynthesis approaches that explore the chemical biosynthetic space. However, the complexity associated with the large combinatorial retrosynthesis design space has often been recognized as the main challenge hindering the approach. Here, we provide RetroPath2.0, an automated open source workflow for retrosynthesis based on generalized reaction rules that perform the retrosynthesis search from chassis to target through an efficient and well-controlled protocol. Its easiness of use and the versatility of its applications make of this tool a valuable addition into the biological engineer bench desk. We show through several examples the application of the workflow to biotechnological relevant problems, including the identification of alternative biosynthetic routes through enzyme promiscuity; or the development of biosensors. We demonstrate in that way the ability of the workflow to streamline retrosynthesis pathway design and its major role in reshaping the design, build, test and learn pipeline by driving the process toward the objective of optimizing bioproduction. The RetroPath2.0 workflow is built using tools developed by the bioinformatics and cheminformatics community, because it is open source we anticipate community contributions will likely expand further the features of the workflow.HighlightsState-of-the-art Computer-Aided Design retrosynthesis solutions lack open source and ease of useWe propose RetroPath2.0 a modular and open-source workflow to perform retrosynthesisRetroPath2.0 computes reaction network between Source and Sink sets of compoundsRetroPath2.0 is distributed as a KNIME workflow for desktop computersRetroPath2.0 is ready-for-use and distributed with reaction rulesFundingThis work was supported by the French National Research Agency [ANR-15-CE1-0008], the Biotechnology and Biological Sciences Research Council, Centre for synthetic biology of fine and speciality chemicals [BB/M017702/1]; Synthetic Biology Applications for Protective Materials [EP/N025504/1], and GIP Genopole.

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Omics-Driven Biotechnology for Industrial Applications

Frontiers in Bioengineering and Biotechnology ◽

10.3389/fbioe.2021.613307 ◽

2021 ◽

Vol 9 ◽

Author(s):

Bashar Amer ◽

Edward E. K. Baidoo

Keyword(s):

Metabolic Engineering ◽

Systems Biology ◽

Synthetic Biology ◽

Metabolic Networks ◽

Industrial Applications ◽

Omics Technologies ◽

Food Biotechnology ◽

Food And Agriculture ◽

Pros And Cons ◽

The Impact

Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on “omics” driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in “omics” technologies, compare the pros and cons of the different “omics” technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of “omics” technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of “omics” technologies to agricultural and food biotechnology, and review the impact of “omics” on current COVID-19 research.

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Exploring Synthetic and Systems Biology at the University of Edinburgh

Biochemical Society Transactions ◽

10.1042/bst20160006 ◽

2016 ◽

Vol 44 (3) ◽

pp. 692-695 ◽

Cited By ~ 4

Author(s):

Liz Fletcher ◽

Susan Rosser ◽

Alistair Elfick

Keyword(s):

Biological Sciences ◽

Systems Biology ◽

Synthetic Biology ◽

Research Council ◽

Common Interest ◽

Industrial Biotechnology ◽

Physical Sciences ◽

University Of Edinburgh ◽

The University ◽

Research Councils

The Centre for Synthetic and Systems Biology ('SynthSys') was originally established in 2007 as the Centre for Integrative Systems Biology, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC). Today, SynthSys embraces an extensive multidisciplinary community of more than 200 researchers from across the University with a common interest in synthetic and systems biology. Our research is broad and deep, addressing a diversity of scientific questions, with wide ranging impact. We bring together the power of synthetic biology and systems approaches to focus on three core thematic areas: industrial biotechnology, agriculture and the environment, and medicine and healthcare. In October 2015, we opened a newly refurbished building as a physical hub for our new U.K. Centre for Mammalian Synthetic Biology funded by the BBSRC/EPSRC/MRC as part of the U.K. Research Councils' Synthetic Biology for Growth programme.

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Developing synthetic biology for industrial biotechnology applications

Biochemical Society Transactions ◽

10.1042/bst20190349 ◽

2020 ◽

Vol 48 (1) ◽

pp. 113-122

Author(s):

Lionel Clarke ◽

Richard Kitney

Keyword(s):

Synthetic Biology ◽

Scale Up ◽

Private Investment ◽

Consumer Products ◽

Industrial Biotechnology ◽

Investment Activity ◽

Ongoing Research ◽

The Us ◽

Start Ups ◽

The Impact

Since the beginning of the 21st Century, synthetic biology has established itself as an effective technological approach to design and engineer biological systems. Whilst research and investment continues to develop the understanding, control and engineering infrastructural platforms necessary to tackle ever more challenging systems — and to increase the precision, robustness, speed and affordability of existing solutions — hundreds of start-up companies, predominantly in the US and UK, are already translating learnings and potential applications into commercially viable tools, services and products. Start-ups and SMEs have been the predominant channel for synthetic biology commercialisation to date, facilitating rapid response to changing societal interests and market pull arising from increasing awareness of health and global sustainability issues. Private investment in start-ups across the US and UK is increasing rapidly and now totals over $12bn. Health-related biotechnology applications have dominated the commercialisation of products to date, but significant opportunities for the production of bio-derived materials and chemicals, including consumer products, are now being developed. Synthetic biology start-ups developing tools and services account for between 10% (in the UK) and ∼25% (in the US) of private investment activity. Around 20% of synthetic biology start-ups address industrial biotechnology targets, but currently, only attract ∼11% private investment. Adopting a more networked approach — linking specialists, infrastructure and ongoing research to de-risk the economic challenges of scale-up and supported by an effective long-term funding strategy — is set to transform the impact of synthetic biology and industrial biotechnology in the bioeconomy.

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