Design and Validation of Tools for Microbial Synthetic Biology Applications

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Synthetic Biology and Systems Biology".

Deadline for manuscript submissions: closed (15 October 2020) | Viewed by 32056

Special Issue Editors


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Guest Editor
i3S – Instituto de Investigação e Inovação em Saúde & IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
Interests: synthetic biology; microbiology; molecular biology; cyanobacteria; SB tools; regulatory elements; value-added compounds; compatible solutes; biocatalysis; RT-qPCR

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Co-Guest Editor
Institution: School of Biological Sciences & Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
Interests: synthetic biology; microbiology; molecular biology; protein engineering; synthetic biological circuits; logic gates; regulatory elements; SB tools

Special Issue Information

Dear Colleagues,

Synthetic biology (SB) has revolutionized the way scientists manipulate biological systems, applying engineering principles to modify biological functions or to design new ones. This paradigm is implemented by the construction of synthetic devices/circuits, artificial biological pathways, and organisms. The emergence of the SB field is having a profound impact on applied and fundamental science spanning a broad spectrum of areas, ranging from biology and chemistry to mathematics and computer engineering.

The successful implementation of SB applications using microorganisms as chassis largely relies on the existing toolboxes that need to be custom-built since the performance of biological parts and tools is organism-dependent. The forthcoming Special Issue of Life includes reviews, original research manuscripts, and short communications focusing on the design and validation of tools for microorganisms, including the universal chassis Escherichia coli, Bacillus subtilis and Sacharomyces cerevisae, also extended to other bacteria (e.g., Streptomyces and Cyanobacteria) and microalgae. In addition, special emphasis will be given to the validation of biological parts (e.g., regulatory elements), genome-editing tools as well as prediction tools (e.g., genome-scale metabolic models) and computer-aided design (CAD) tools. Papers focusing on the development of cloning suites or high-throughput validation methods are also welcome.

As Guest Editors, we cordially invite researchers to submit their recent advances in the field to this Special Issue of Life.

Dr. Catarina C. Pacheco
Dr. Filipe Pinto
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Synthetic biology
  • Regulatory elements
  • Assembly platforms and cloning suites
  • Genome editing tools
  • Computer-aided design (CAD) and prediction tools

Published Papers (6 papers)

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Editorial

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2 pages, 176 KiB  
Editorial
Design and Validation of Tools for Microbial Synthetic Biology Applications
by Catarina C. Pacheco and Filipe Pinto
Life 2021, 11(8), 739; https://doi.org/10.3390/life11080739 - 24 Jul 2021
Viewed by 1409
Abstract
Synthetic Biology (SynBio) is a multidisciplinary field that brings together science, technology and engineering to expedite the design, creation and modification of genetic materials to be applied in living organisms or in vitro systems [...] Full article

Research

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15 pages, 2706 KiB  
Article
A Strategy for Combinatorial Cavity Design in De Novo Proteins
by Christina Karas and Michael Hecht
Life 2020, 10(2), 9; https://doi.org/10.3390/life10020009 - 23 Jan 2020
Cited by 9 | Viewed by 4054
Abstract
Protein sequence space is vast; nature uses only an infinitesimal fraction of possible sequences to sustain life. Are there solutions to biological problems other than those provided by nature? Can we create artificial proteins that sustain life? To investigate these questions, we have [...] Read more.
Protein sequence space is vast; nature uses only an infinitesimal fraction of possible sequences to sustain life. Are there solutions to biological problems other than those provided by nature? Can we create artificial proteins that sustain life? To investigate these questions, we have created combinatorial collections, or libraries, of novel sequences with no homology to those found in living organisms. Previously designed libraries contained numerous functional proteins. However, they often formed dynamic, rather than well-ordered structures, which complicated structural and mechanistic characterization. To address this challenge, we describe the development of new libraries based on the de novo protein S-824, a 4-helix bundle with a very stable 3-dimensional structure. Distinct from previous libraries, we targeted variability to a specific region of the protein, seeking to create potential functional sites. By characterizing variant proteins from this library, we demonstrate that the S-824 scaffold tolerates diverse amino acid substitutions in a putative cavity, including buried polar residues suitable for catalysis. We designed and created a DNA library encoding 1.7 × 106 unique protein sequences. This new library of stable de novo α-helical proteins is well suited for screens and selections for a range of functional activities in vitro and in vivo. Full article
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Review

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16 pages, 2880 KiB  
Review
CRISPR-Cas9: A Powerful Tool to Efficiently Engineer Saccharomyces cerevisiae
by João Rainha, Joana L. Rodrigues and Lígia R. Rodrigues
Life 2021, 11(1), 13; https://doi.org/10.3390/life11010013 - 26 Dec 2020
Cited by 22 | Viewed by 12022
Abstract
Saccharomyces cerevisiae has been for a long time a common model for fundamental biological studies and a popular biotechnological engineering platform to produce chemicals, fuels, and pharmaceuticals due to its peculiar characteristics. Both lines of research require an effective editing of the native [...] Read more.
Saccharomyces cerevisiae has been for a long time a common model for fundamental biological studies and a popular biotechnological engineering platform to produce chemicals, fuels, and pharmaceuticals due to its peculiar characteristics. Both lines of research require an effective editing of the native genetic elements or the inclusion of heterologous pathways into the yeast genome. Although S. cerevisiae is a well-known host with several molecular biology tools available, a more precise tool is still needed. The clustered, regularly interspaced, short palindromic repeats–associated Cas9 (CRISPR-Cas9) system is a current, widespread genome editing tool. The implementation of a reprogrammable, precise, and specific method, such as CRISPR-Cas9, to edit the S. cerevisiae genome has revolutionized laboratory practices. Herein, we describe and discuss some applications of the CRISPR-Cas9 system in S. cerevisiae from simple gene knockouts to more complex processes such as artificial heterologous pathway integration, transcriptional regulation, or tolerance engineering. Full article
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11 pages, 1797 KiB  
Review
Bioluminescence-Driven Optogenetics
by Macià Sureda-Vives and Karen S. Sarkisyan
Life 2020, 10(12), 318; https://doi.org/10.3390/life10120318 - 28 Nov 2020
Cited by 9 | Viewed by 4808
Abstract
Bioluminescence-based technologies are among the most commonly used methods to quantify and visualise physiology at the cellular and organismal levels. However, the potential of bioluminescence beyond reporter technologies remains largely unexplored. Here, we provide an overview of the emerging approaches employing bioluminescence as [...] Read more.
Bioluminescence-based technologies are among the most commonly used methods to quantify and visualise physiology at the cellular and organismal levels. However, the potential of bioluminescence beyond reporter technologies remains largely unexplored. Here, we provide an overview of the emerging approaches employing bioluminescence as a biological light source that triggers physiological events and controls cell behaviour and discuss its possible future application in synthetic biology. Full article
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20 pages, 1066 KiB  
Review
The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels
by Maria Priscila Lacerda, Eun Joong Oh and Carrie Eckert
Life 2020, 10(11), 299; https://doi.org/10.3390/life10110299 - 21 Nov 2020
Cited by 21 | Viewed by 4205
Abstract
Microorganisms are effective platforms for the production of a variety of chemicals including biofuels, commodity chemicals, polymers and other natural products. However, deep cellular understanding is required for improvement of current biofuel cell factories to truly transform the Bioeconomy. Modifications in microbial metabolic [...] Read more.
Microorganisms are effective platforms for the production of a variety of chemicals including biofuels, commodity chemicals, polymers and other natural products. However, deep cellular understanding is required for improvement of current biofuel cell factories to truly transform the Bioeconomy. Modifications in microbial metabolic pathways and increased resistance to various types of stress caused by the production of these chemicals are crucial in the generation of robust and efficient production hosts. Recent advances in systems and synthetic biology provide new tools for metabolic engineering to design strategies and construct optimal biocatalysts for the sustainable production of desired chemicals, especially in the case of ethanol and fatty acid production. Yeast is an efficient producer of bioethanol and most of the available synthetic biology tools have been developed for the industrial yeast Saccharomyces cerevisiae. Non-conventional yeast systems have several advantageous characteristics that are not easily engineered such as ethanol tolerance, low pH tolerance, thermotolerance, inhibitor tolerance, genetic diversity and so forth. Currently, synthetic biology is still in its initial steps for studies in non-conventional yeasts such as Yarrowia lipolytica, Kluyveromyces marxianus, Issatchenkia orientalis and Pichia pastoris. Therefore, the development and application of advanced synthetic engineering tools must also focus on these underexploited, non-conventional yeast species. Herein, we review the basic synthetic biology tools that can be applied to the standard S. cerevisiae model strain, as well as those that have been developed for non-conventional yeasts. In addition, we will discuss the recent advances employed to develop non-conventional yeast strains that are efficient for the production of a variety of chemicals through the use of metabolic engineering and synthetic biology. Full article
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21 pages, 1847 KiB  
Review
Synthetic Biology Approaches to Engineer Saccharomyces cerevisiae towards the Industrial Production of Valuable Polyphenolic Compounds
by João Rainha, Daniela Gomes, Lígia R. Rodrigues and Joana L. Rodrigues
Life 2020, 10(5), 56; https://doi.org/10.3390/life10050056 - 2 May 2020
Cited by 21 | Viewed by 4767
Abstract
Polyphenols are plant secondary metabolites with diverse biological and potential therapeutic activities such as antioxidant, anti-inflammatory and anticancer, among others. However, their extraction from the native plants is not enough to satisfy the increasing demand for this type of compounds. The development of [...] Read more.
Polyphenols are plant secondary metabolites with diverse biological and potential therapeutic activities such as antioxidant, anti-inflammatory and anticancer, among others. However, their extraction from the native plants is not enough to satisfy the increasing demand for this type of compounds. The development of microbial cell factories to effectively produce polyphenols may represent the most attractive solution to overcome this limitation and produce high amounts of these bioactive molecules. With the advances in the synthetic biology field, the development of efficient microbial cell factories has become easier, largely due to the development of the molecular biology techniques and by the identification of novel isoenzymes in plants or simpler organisms to construct the heterologous pathways. Furthermore, efforts have been made to make the process more profitable through improvements in the host chassis. In this review, advances in the production of polyphenols by genetically engineered Saccharomyces cerevisiae as well as by synthetic biology and metabolic engineering approaches to improve the production of these compounds at industrial settings are discussed. Full article
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