scholarly journals Engineering yeast shikimate pathway towards production of aromatics: rational design of a chassis cell using systems and synthetic biology

2016 ◽  
Author(s):  
Nils Averesch
Keyword(s):  
Synthetic Biology ◽  
Rational Design ◽  
Shikimate Pathway

Evolving protocells to prototissues: rational design of a missing link

2013 ◽  
Vol 41 (5) ◽  
pp. 1159-1165 ◽  
Author(s):  
Shiksha Mantri ◽  
K. Tanuj Sapra
Keyword(s):  
Synthetic Biology ◽  
Rational Design ◽  
Structural Elements ◽  
Bottom Up ◽  
Missing Link ◽  
Hierarchical Assembly ◽  
Artificial Cell

Realization of a functional artificial cell, the so-called protocell, is a major challenge posed by synthetic biology. A subsequent goal is to use the protocellular units for the bottom-up assembly of prototissues. There is, however, a looming chasm in our knowledge between protocells and prototissues. In the present paper, we give a brief overview of the work on protocells to date, followed by a discussion on the rational design of key structural elements specific to linking two protocellular bilayers. We propose that designing synthetic parts capable of simultaneous insertion into two bilayers may be crucial in the hierarchical assembly of protocells into a functional prototissue.

scholarly journals Mycobacterium tuberculosis Shikimate Pathway Enzymes as Targets for the Rational Design of Anti-Tuberculosis Drugs

Molecules ◽  
2020 ◽  
Vol 25 (6) ◽  
pp. 1259 ◽  
Author(s):  
José E. S. Nunes ◽  
Mario A. Duque ◽  
Talita F. de Freitas ◽  
Luiza Galina ◽  
Luis F. S. M. Timmers ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Rational Design ◽  
Shikimate Pathway ◽  
Chemotherapeutic Agents ◽  
New Drugs ◽  
Patient Treatment ◽  
Drug Resistant ◽  
Mycobacterium Tuberculosis Infection ◽  
Selective Toxicity ◽  
Prophylactic Measures

Roughly a third of the world’s population is estimated to have latent Mycobacterium tuberculosis infection, being at risk of developing active tuberculosis (TB) during their lifetime. Given the inefficacy of prophylactic measures and the increase of drug-resistant M. tuberculosis strains, there is a clear and urgent need for the development of new and more efficient chemotherapeutic agents, with selective toxicity, to be implemented on patient treatment. The component enzymes of the shikimate pathway, which is essential in mycobacteria and absent in humans, stand as attractive and potential targets for the development of new drugs to treat TB. This review gives an update on published work on the enzymes of the shikimate pathway and some insight on what can be potentially explored towards selective drug development.

Synthetic biology: insights into biological computation

2016 ◽  
Vol 8 (4) ◽  
pp. 518-532 ◽  
Author(s):  
Romilde Manzoni ◽  
Arturo Urrios ◽  
Silvia Velazquez-Garcia ◽  
Eulàlia de Nadal ◽  
Francesc Posas
Keyword(s):  
Synthetic Biology ◽  
Rational Design ◽  
Biological Systems ◽  
Biological Computation

Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology.

scholarly journals Functional Characterization by Genetic Complementation of aroB-Encoded Dehydroquinate Synthase from Mycobacterium tuberculosis H37Rv and Its Heterologous Expression and Purification

2007 ◽  
Vol 189 (17) ◽  
pp. 6246-6252 ◽  
Author(s):  
Jordana Dutra de Mendonça ◽  
Fernanda Ely ◽  
Mario Sergio Palma ◽  
Jeverson Frazzon ◽  
Luiz Augusto Basso ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Drug Targets ◽  
Rational Design ◽  
Functional Characterization ◽  
Pcr Amplification ◽  
Shikimate Pathway ◽  
Aromatic Amino Acids ◽  
Multidrug Resistant ◽  
Genetic Complementation ◽  
Dehydroquinate Synthase

ABSTRACT The recent recrudescence of Mycobacterium tuberculosis infection and the emergence of multidrug-resistant strains have created an urgent need for new therapeutics against tuberculosis. The enzymes of the shikimate pathway are attractive drug targets because this route is absent in mammals and, in M. tuberculosis, it is essential for pathogen viability. This pathway leads to the biosynthesis of aromatic compounds, including aromatic amino acids, and it is found in plants, fungi, bacteria, and apicomplexan parasites. The aroB-encoded enzyme dehydroquinate synthase is the second enzyme of this pathway, and it catalyzes the cyclization of 3-deoxy-d-arabino-heptulosonate-7-phosphate in 3-dehydroquinate. Here we describe the PCR amplification and cloning of the aroB gene and the overexpression and purification of its product, dehydroquinate synthase, to homogeneity. In order to probe where the recombinant dehydroquinate synthase was active, genetic complementation studies were performed. The Escherichia coli AB2847 mutant was used to demonstrate that the plasmid construction was able to repair the mutants, allowing them to grow in minimal medium devoid of aromatic compound supplementation. In addition, homogeneous recombinant M. tuberculosis dehydroquinate synthase was active in the absence of other enzymes, showing that it is homomeric. These results will support the structural studies with M. tuberculosis dehydroquinate synthase that are essential for the rational design of antimycobacterial agents.

scholarly journals Intrinsic limitations in mainstream methods of identifying network motifs in biology

2018 ◽  
Author(s):  
James Fodor ◽  
Michael Brand ◽  
Rebecca J Stones ◽  
Ashley M Buckle
Keyword(s):  
Gene Regulation ◽  
Statistical Analysis ◽  
Synthetic Biology ◽  
Biological Networks ◽  
Rational Design ◽  
Statistical Significance ◽  
Biological Systems ◽  
Network Motifs ◽  
Motif Identification ◽  
Spurious Results

Network motifs are connectivity structures that occur with significantly higher frequency than chance, and are thought to play important roles in complex biological networks, for example in gene regulation, interactomes, and metabolomes. Network motifs may also become pivotal in the rational design and engineering of complex biological systems underpinning the field of synthetic biology. Distinguishing true motifs from arbitrary substructures, however, remains a challenge. Here we demonstrate both theoretically and empirically that implicit assumptions present in mainstream methods for motif identification do not necessarily hold, with the ramification that motif studies using these mainstream methods are less able to effectively differentiate between spurious results and events of true statistical significance than is often presented. We show that these difficulties cannot be overcome without revising the methods of statistical analysis used to identify motifs. The implications of these findings are therefore far-reaching across diverse areas of biology.

scholarly journals Synthetic biology: paving the way with novel drug delivery

2019 ◽  
Vol 41 (3) ◽  
pp. 24-27 ◽  
Author(s):  
Lucas M. Bush ◽  
Chelsea Gibbs ◽  
Tara L. Deans
Keyword(s):  
Gene Expression ◽  
Drug Delivery ◽  
Synthetic Biology ◽  
Rational Design ◽  
Control Cell ◽  
Regulation Of Gene Expression ◽  
Modern Technology ◽  
Gene Circuits ◽  
Basic Concepts ◽  
Novel Drug

Synthetic biology is a multidisciplinary field that focuses on the rational design and construction of novel genetic tools for the purpose of engineering cells to behave in controllable and predictable ways. The promise of this modern technology relies on our understanding of basic genetics and gene expression to engineer cells with unique functions. This is accomplished by designing biological parts and assembling them into higher-order gene circuits that control cell operations through tight regulation of gene expression, effectively reprogramming and rewiring the cells. In this article, we review the basic concepts of gene expression, discuss the framework of how synthetic biologists reprogram cells and outline how cells can be engineered to function as new vehicles for delivering therapeutic proteins.

scholarly journals Applying Synthetic Biology with Rational Design to Nature’s Greatest Challenges: Bioengineering Immunotherapeutics for the Treatment of Glioblastoma

Immuno ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 40-51
Author(s):  
Leila A. Mashouf ◽  
Janet Y. Wu ◽  
Pavan Shah ◽  
Nivedha Kannapadi ◽  
Michael Lim
Keyword(s):  
Synthetic Biology ◽  
Consumer Goods ◽  
Rational Design ◽  
Significant Progress ◽  
Creative Development ◽  
Adequate Treatment ◽  
Treatment Development ◽  
Food And Agriculture

Improvements in bioengineering methodology and tools have allowed for significant progress in the development of therapeutics and diagnostics in medicine, as well as progress in many other diverse industries, such as materials manufacturing, food and agriculture, and consumer goods. Glioblastomas present significant challenges to adequate treatment, in part due to their immune-evasive and manipulative nature. Rational-design bioengineering using novel scaffolds, biomaterials, and inspiration across disciplines can push the boundaries in treatment development to create effective therapeutics for glioblastomas. In this review, we will discuss bioengineering strategies currently applied across diseases and disciplines to inspire creative development for GBM immunotherapies.

scholarly journals Rational design of peptide-based building blocks for nanoscience and synthetic biology

2009 ◽  
Vol 143 ◽  
pp. 305 ◽  
Author(s):  
Craig T. Armstrong ◽  
Aimee L. Boyle ◽  
Elizabeth H. C. Bromley ◽  
Zahra N. Mahmoud ◽  
Lisa Smith ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Rational Design ◽  
Building Blocks
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