Search results for "Synthetic Biology"
showing 10 items of 73 documents
Polarity and bioelectrical patterning in a linear chain of non-excitable cells
2020
Abstract Polarity in multicellular systems is influenced by bioelectrical signals because electric potentials can act as spatio-temporal patterns for other biochemical processes that eventually emerge as long-lasting biological outcomes. We study the role of the electric potential in establishing head-tail polarity for the case of a chain of non-excitable cells. This biophysical model incorporates both single-cell (membrane ion channels) and multicellular (intercellular gap junctions) characteristics. The results are presented in the form of a bioelectrical phase space that complements traditional biochemical approaches and provides qualitative insights for the case of anterior/posterior po…
Dual film-like organelles enable spatial separation of orthogonal eukaryotic translation
2021
Summary Engineering new functionality into living eukaryotic systems by enzyme evolution or de novo protein design is a formidable challenge. Cells do not rely exclusively on DNA-based evolution to generate new functionality but often utilize membrane encapsulation or formation of membraneless organelles to separate distinct molecular processes that execute complex operations. Applying this principle and the concept of two-dimensional phase separation, we develop film-like synthetic organelles that support protein translation on the surfaces of various cellular membranes. These sub-resolution synthetic films provide a path to make functionally distinct enzymes within the same cell. We use t…
Natural or synthetic nucleic acids encapsulated in a closed cavity of amphiphiles
2013
In this review some aspects of the interactions of organized structures of amphiphiles with natural or synthetic DNAs are briefly considered. In particular DNAs encapsulated in closed cavities of amphiphiles, specifically giant vesicles and water-in-oil droplets and reverse micelles, are dealt with. Two main applications of giant vesicles are reviewed in detail, namely their use as microreactors where reactions can be followed by optical microscopy on a single vesicle and in synthetic biology as protocell models or as potential semi-synthetic ‘‘living’’ cells. Water-in-oil droplets uses for rapid and relatively low-cost DNA amplification by PCR reaction are described as well as for in vitro…
Accelerated evolution of a minimal 63–amino acid dual transcription factor
2020
Transcription factors control gene expression in all life. This raises the question of what is the smallest protein that can support such activity. In nature, Cro from bacteriophage λ is one of the smallest known repressors (66 amino acids), and activators are typically much larger (e.g., λ cI, 237 amino acids). Previous efforts to engineer a minimal activator from λ Cro resulted in no activity in vivo in cells. In this study, we show that directed evolution results in a new Cro activator-repressor that functions as efficiently as λ cI in vivo. To achieve this, we develop phagemid-assisted continuous evolution (PACEmid). We find that a peptide as small as 63 amino acids functions efficientl…
Responsibility and intellectual property in synthetic biology: A proposal for using Responsible Research and Innovation as a basic framework for inte…
2015
Synthetic biology (SynBio) is an engineering view of biotechnology that has the potential to increase the number and industrial utility of biotechnological applications by implementing engineering principles such as standardization and modularity. The boundaries between SynBio, biotechnology, and metabolic engineering are not always clear, but assessing SynBio in a wider sense—that of modeling‐based biotechnology and/or “sophisticated” metabolic engineering—we find that a significant number of applications and research articles have been generated in the past few years [1]. One of the best‐known examples is that of a synthetic pathway for producing artemisinic acid, a precursor to the antim…
Engineering a Circular Riboregulator in Escherichia coli
2020
RNAs of different shapes and sizes, natural or synthetic, can regulate gene expression in prokaryotes and eukaryotes. Circular RNAs have recently appeared to be more widespread than previously thought, but their role in prokaryotes remains elusive. Here, by inserting a riboregulatory sequence within a group I permuted intron-exon ribozyme, we created a small noncoding RNA that self-splices to produce a circular riboregulator in Escherichia coli . We showed that the resulting riboregulator can trans -activate gene expression by interacting with a cis -repressed messenger RNA. We characterized the system with a fluorescent reporter and with an antibiotic resistance marker, and we modeled thi…
Expanding the chemical scope of RNA:methyltransferases to site-specific alkynylation of RNA for click labeling.
2010
This work identifies the combination of enzymatic transfer and click labeling as an efficient method for the site-specific tagging of RNA molecules for biophysical studies. A double-activated analog of the ubiquitous co-substrate S-adenosyl-l-methionine was employed to enzymatically transfer a five carbon chain containing a terminal alkynyl moiety onto RNA. The tRNA:methyltransferase Trm1 transferred the extended alkynyl moiety to its natural target, the N2 of guanosine 26 in tRNA(Phe). LC/MS and LC/MS/MS techniques were used to detect and characterize the modified nucleoside as well as its cycloaddition product with a fluorescent azide. The latter resulted from a labeling reaction via Cu(I…
A synthetic biology approach for the fabrication of functional (fluorescent magnetic) bioorganic–inorganic hybrid materials in sponge primmorphs
2020
During evolution, sponges (Porifera) have honed the genetic toolbox and biosynthetic mechanisms for the fabrication of siliceous skeletal components (spicules). Spicules carry a protein scaffold embedded within biogenic silica (biosilica) and feature an amazing range of optical, structural, and mechanical properties. Thus, it is tempting to explore the low-energy synthetic pathways of spiculogenesis for the fabrication of innovative hybrid materials. In this synthetic biology approach, the uptake of multifunctional nonbiogenic nanoparticles (fluorescent, superparamagnetic) by spicule-forming cells of bioreactor-cultivated sponge primmorphs provides access to spiculogenesis. The ingested nan…
Synthetic Biology in Action
2014
Last decade has witnessed remarkable advances towards the engineering of life. The examples range from the design of an efficient cellular factory for the semi-synthesis of the antimalarial drug artemisinin, to the chemical synthesis of chromosomes, both bacterial and eukaryotic. In parallel, advances in the deep characterization of cell machineries in the simplest cells show that we are very far of fully understanding the regulation of metabolic and genetic circuits. Biological emergent properties and noise may suppose an obstacle for predictive design. Besides the obvious biotechnological benefits of synthetic biology, the path towards the artificial cell will report new insights on the e…
What Is Life?
2014
Despite the difficulty of defining a living being, biological sciences have considerably advanced. Today many authors feel the need to revisit the issue of the definition of life, among other reasons, because we are very close to have a second example of life. This life will not be the direct result of more than 3,500 million years of evolution, but the outcome of a project of synthetic biology in a laboratory. The fact that evolution has explored only a small part of the possible may pave the way towards alternative artificial lives. Focusing on the nature of life makes us more critical with the Cartesian comparisons between cells and machines. At the same time, progress in synthetic biolo…