Xenobiology Incase
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Xenobiology is an emergent discipline that implies the redesign of biology by introducing e.g. non-traditional building blocks into biochemical systems. Together with our guest editors Ned Budisa, Vladimir Kubyshkin (both University of Manitoba), and Markus Schmidt (Biofaction), we are proud to publish this Special Collection on Xenobiology to highlight the important achievements this field has made in the recent years.
Xenobiology is the science of estranged life forms . At the heart of this science is the idea of creating an orthogonal biological system that would be incompatible with natural genetic systems based on unusual biochemistries delivered by chemical compounds of mostly anthropogenic origin. Xenobiology enables us to create and study strange new life forms, “aliens”. In this research, they are not treated as strict extraterrestrial lifeforms. Such “aliens” are not designed in the way science fiction books do it, but in terms of enlightened science, design and engineering. More information on our special collection of articles on xenobiology can be found in the editorial by N. Budisa, V. Kubyshkin and M. Schmidt.
As shown for the model peptide NFGAIL , the introduction of different fluorinated phenylalanine derivatives leads to specific amyloid-folding kinetics through an alteration in hydrophobicity and changes in their α-frameworks. This is represented by the clock, as its hand (the “F” for fluorine) determines the self-assembly process. The extent of fluorination, illustrated as potential plots, acts as a dimension of change not only for aggregation kinetics, but also for the morphology of resulting fibrils, as revealed by TEM micrographs. More information can be found in the full paper by B. Koksch et al. The picture was created by S.C., Helmut Fouquet, J.M., M.B., R.R.N. and B.K.
The alien life : A long journey towards estranged life forms begins here! How could we think of it in terms of science?
Competition experiments : “iGEM-Synthetic Biology” is a student-centered, research-based teaching format for xenobiology. Students conduct their own experiments in an interdisciplinary team with a focus on participation in an international competition. Such formats motivate students to show the highest performance and are possibly the best way to teach novel emerging research fields within the Humboldtian model of higher education.
Possible building blocks of life : According to the multiple realizability thesis in the philosophy of science, there should exist radically different ways to build systems with the functions we value in complex life. Xenobiology's exploration of the viability of unfamiliar biochemistries provides the first serious empirical test of this idea.
Future advances in xenobiology will require orthogonal genetic polymers that can replicate inside living cells. This viewpoint highlights a possible strategy for converting synthetic biology information encoded in DNA into synthetic genetic polymers that do not base pair with natural DNA and RNA.
Nanoreactors meet living systems . Artificial organelles, synthetic analogues of natural organelles, are gaining interest for the correction of dysfunctional intracellular processes and the addition of novel functionalities to living systems. This review outlines the different strategies via which these mostly nanosized catalytic compartments are produced and integrated with living cells.
Multifunctional : Tryptophan synthase (TrpS) natively catalyzes the formation of tryptophan but also possesses remarkable promiscuous activity for synthesizing a wide range of noncanonical amino acids (ncAAs). This review looks at TrpS as a ncAA synthase, from the characterization of its broad substrate scope via efforts to expand its non-natural chemistry to applications in synthesizing diverse natural and xenobiotic compounds.
Outside the box : Xenoelements can be incorporated into the chemistry of microbial cells by combining several approaches. Engineered hosts are programmed through neometabolism to accept nonbiological atoms, incorporated into xenometabolites. Some of these molecules are added-value chemicals in themselves; others (e. g., modified amino acids) can be integrated into proteins to explore emergence of novel functions.
A weighty matter : Using isotopes or missing counterparts of the key atoms that make cells will allow us to highlight unexpected functions that contribute to the “animation” of life's chemistry.
Expansion of nature's toolkit by genetically encoded amino acids has enabled the production of proteins with tailored electronic and structural properties. This minireview highlights recent studies showing that noncanonical amino acids are powerful tools for capturing short-lived protein intermediates and accessing novel function.
Trying something different : Specially designed noncanonical amino acids (ncAAs) are highly useful building blocks. This minireview explores how noncanonical chemical groups can be incorporated into proteins, and how these methodologies may be applied in studies of post-translational modifications and synthetic biosafety.
Vaccine variations : This article reviews the utility of genetic code expansion as an emerging tool for the development of vaccines. It highlights how the incorporation of immunogenic noncanonical amino acids (ncAA) can aid in eliciting immune responses against adverse self-proteins and highlights the potential of an expanded genetic code for the construction of live-attenuated virus vaccines.
Unlimited : Current research on artificial enzymes conclusively shows that we are not limited to nature's biocatalytic repertoire. Functional xenobiology, that is, the implementation of new-to-nature reactions in vivo, will open up a plethora of novel applications and has the potential for transformative biotechnological innovation. Herein, we highlight current challenges and future opportunities for xenobiotic reactions in living cells.
Taking control ! Translation initiation can be engineered to occur at any non-AUG codon using several different strategies both in vitro and in vivo. The α-amine of the initiating amino acid is not required for elongation which allows for a diverse range of molecules to be incorporated.
Removing the limits : The recent intracellular biocatalytic synthesis of noncanonical amino acids coupled with genetic-code expansion in situ has been applied as a way to overcome the limitations imposed by the external supply of ncAAs. This minireview illustrates the most significant advances towards this goal and their implications for biotechnological uses.
A better fit : The substitution of halogenated tyrosine for tyrosine at multiple selective sites in an antibody improves antigen binding. Some of the halogen atoms thus introduced fill vacant space between antigen and antibody, and thus enhance the shape complementarity at the molecular interface.
Genetic code expansion on demand by combining the amber suppression technology with the T-REx system. Amber suppression is regulated by the T-REx system to switch on the tRNA production and/or the synthetase translation only when needed, thus minimizing the risk of adverse effects for the cells resulting from over-production of unused tRNA or synthetase.
Expanding biotransformations : Several metal-binding noncanonical amino acids have been incorporated into protein scaffolds to create artificial metalloenzymes. We introduced 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQAla) into lactococcal multidrug-resistance regulator (LmrR) and complexed it with several transition metal ions such as Cu II , Zn II and Rh III to showcase its catalytic potential in a variety of different reactions.
How to cook primordial soup ? Synergistic interactions are prevalent in catalytic amyloids providing insight into how early prebiotic peptides might have found productive combinations of functional groups to become the precursors of modern-day enzymes.
Fluorinated organic molecules are of great value both for agriculture and medicine. However, fluorine chemistry is expensive and harmful to the environment. Natural products are at a premium and are only produced by a handful of organisms. For the first time, an engineered E. coli is presented with the capacity to produce a naturally occurring fluorinated molecule.
C−H Amination via Nitrene Transfer Catalyzed by Mononuclear Non-Heme Iron-Dependent Enzymes
Direct optical perturbation of cellular ATP levels is achieved by substituting the essential lysine of E. coli adenylate kinase with a hydroxycoumarin-protected lysine through unnatural amino acid mutagenesis. The caged lysine residue renders the kinase inactive until photolysis reactivates it in both E. coli and mammalian cells.
A stable ladder : Thermal and spectroscopic analyses of xylose (XyNA) and deoxyxylose nucleic acids (dXyNA) indicate the formation of stable hairpin structures. The solution structure of a fully modified dXyNA hairpin indicates the structural preference for a ladder-like stem with a noncanonical loop.
Quantifying the distance : If two organisms operate under different genetic codes, how likely is that they could still properly interpret each other's genes? We introduce a versatile metric to quantify the distance between the different genetic codes. It can calculate the distance (dissimilarity) between genetic codes and can be applied with the 20 canonical but also noncanonical amino acids.
F for formation : This study introduces systematic fluorination as a tool to investigate the nature of amyloid formation as shown for the model peptide NFGAIL. Modulation of hydrophobicity and the σ-framework of the Phe residue trough fluorine and iodine led to different amyloid folding kinetics. TEM and SAXS studies revealed the presence of amyloid fibrils.
Doing things differently : We have metabolically engineered an E. coli strain by reconfiguring the methionine biosynthetic pathway to create a bacterial system with a trans-sulfuration pathway for in-cell production and incorporation of l -azidohomoalanine. Our system is focused on green, sustainable chemistry, and only requires water, salts, trace elements, and simple carbon sources, pushing towards enzyme chemistry and biotechnology-based production.
Stay where you are ! The Δ ung and Δ dut mutations enable partial incorporation of U residues to DNA instead of T, thus making the helix vulnerable to the action of U-DNA glycosylases. This could suggest a general strategy for curbing the dispersal of recombinant genetic constructs into the environment.
Displaying enzymes and low-affinity binding proteins on the surface of the bacterial cell : A SNAP reporter together with the function-dependent labelling of the cell with cholesterol-linked DNA, allows systematic optimisation of cell display, making it a robust and flexible platform for the systematic evolution of XNA molecular biology.
Mind the gap : Our unnatural base pair (UBP) Ds-Px has promising applications in xenobiology. Here, we present an improved Sanger sequencing method in which our UBPs are detected as clear gaps in sequence peak patterns, thus allowing easy determination of UBP positions. High processivity is also exhibited with three UBPs close together.
Making sense : We quantitatively evaluate the effect of the abundance of competing endogenous tRNAs on the ability of orthogonal tRNA variants to reassign E. coli sense codons. For rarely used codons, a strong correlation exists between tRNA abundance and reassignment efficiency. Our measurements suggest that the Ile AUA codon is a particularly good target for genetic code expansion.
Activity FANAtic : Evaluation of the catalytic potential of xenonucleic acid catalysts (XNAzyme) reveals that 2’-fluoroarabino nucleic acid enzymes (FANAzymes) rival their DNA counterparts at cleaving a chimeric DNA substrate under simulated physiological conditions. This finding has important implications for future applications in synthetic biology and medicine.
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