Xenoglue wins competition
- © Science4Life
The technology of Xenoglue, which originates from our group, won the Science4Life start-up competition. Two represantatives of the Xenoglue-team, Christian Schipp and Tobias Schneider, took the award on the 13.03.2018 and the price money of 1000€. Before that they took part in a two day workshop about startup management.
Xenoglue strives to develop a bio degradable glue, which is based on the natural example of the mussel and is intended for usage in wound healing. Scientist have studied the subject of the mussels adhesion mechanism for decades. (See news from 01.08.2017)
BIOMOD 2017: Gold winning MultiBrane team back from San Francisco!
- © AK Biokatalyse Saba Nojoumi
- © BIOMOD Team
The team MultiBrane of the tu project "iGEM Synthetic Biology" 2017 belongs to the big winners of this year's BIOMOD competition. The research objective was to create a multifunctional membrane for waste water treatment with a particular focus on microplastics & micropollutant removal. The results were very compelling and achieved high visibility in San Francisco, where the BIOMOD jamboree took place at UCSF University. Especially in three categories, MultiBranes convinced the international judges and received a gold medal for their project work:
- 3rd place of the grand prize - overall result
- 3rd place in the best project website and
- 3rd place in the best video category
We would therefore like to express our sincere thanks to Saba Nojoumi and Franz-Josef Schmitt for their dedicated mentoring and support respectively. We also thank Hannah Aring and Nikolaj Koch for their work within the scope of tu projects. With this in mind, we congratulate again and wish all the best to all team members and look forward to the next exciting BIOMOD and iGEM projects in the future.
The project results can be found on the team website .
Towards biological underwater superglue
- © Wiley VCH
Regenerative medicine urgently needs biocompatible adhesives suitable for therapeutic use in the treatment of small bone fractures. Such an adhesive should allow rapid bonding of the bone fragments without the need for the attachment of plates and screws. The use of biological glue from marine mussels (so-called mussel-adhesive proteins, MAPs) - as potential environmentally-friendly bio-inspired adhesives - could be a solution to this problem. In nature, mussel secrets adhesive proteins and efficiently adheres to stone and other inorganic surfaces and even to man-made products such as metal and plastic (e.g. Teflon) materials. The secret of these bio-glues is the presence of catechol groups in the side chain of the non-proteinogenic amino acid L-dopa (L-3,4-dihydroxyphenylalanine) which is produced post-translationally by tyrosine hydroxylation and is capable of surface adhesion.
However, isolation of such bio-glues from natural sources is expensive, inefficient, and it is not possible to produce large amounts of a homogeneous product by imitating post-translational modification machineries. On the other hand, current synthetic chemical or biotechnological synthesis pathways are not efficient. For these reasons, we have endeavored to solve this problem by applying an orthogonal amino acid translation to develop a new concept to produce DOPA-rich underwater adhesive proteins from marine mussels by genetic code expansion.
By using computational design and genetic selection methods, a novel Methanocaldococcus jannaschii tyrosyl-tRNA synthetase-based enzyme was engineered. It activates the photocaged DOPA derivative ortho-nitrobenzyl-Dopa (ONB-DOPA) for incorporation into proteins in response to amber stop codons through orthogonal translation. In this way, mussel proteins are equipped with ONB-DOPA at multiple sites, which introduces spatiotemporal control over their adhesive properties. Exposure to UV light triggers cleavage of the ONB photocage, liberating the adhesive catechol side chain of DOPA. This strategy provides new ways for producing DOPA-based wet adhesives for application in industry and biomedicine with the potential to revolutionize bone surgery and wound healing.
A Super Adhesive Made From Intestinal Bacteria 
Link to publication 
Public resonance in Germany:
Durability and Design 
IDW online 
Synthetic alienation of microbes - "thawing" of the "frozen" code
- © AK Biokatalyse
It is assumed that the genetic code experienced a transition from an ambiguous to a well-defined ("frozen") code, as we know it. During this evolution, the protein translation, which first operated with few amino acids and produced the statistical proteins, developed into a highly accurate machine capable of producing very specific proteins, based on the 20 canonical amino acids. Since the genetic code operates well in many ways (e.g. error minimization, protein folding, and metabolic integration), the fundamental question is, what are the barriers to attempts to change it experimentally? How can they be overcome? We have tried to find an answer and written an essay that is now published in the Biotechnology Journal (link ) with a model that has allowed us to provide "entry points" for noncanonical amino acids in the ribosome protein synthesis cycle as shown above.
Thaw what is frozen
- © N. Budisa
In addition, Dr. Uta Goebel, Deputy Editor of Biotechnology Journal wrote a short news piece (link ) at Advanced Science Website . Genetic code engineering is an important step towards the design of fully synthetic cells, where the natural flow of genetic information (DNA → RNA → Proteins) would be redirected or reorganized, resulting in a biocontainment associated with the "genetic firewall" (i.e. genetic isolation from the 'old' biological world). However, since the genetic code (almost unchanged over the past four billion years) is a fundamental level of biological complexity, any changes in its amino acid repertoire (substitutions, reductions, or expansions) require changes in mechanisms that have caused its conservation ("freezing"). Such experiments require the creation of an artificial ambiguity that should allow the inclusion of a new amino acid in its repertoire.
Reprogrammed Protein Translation with Trifluoroethylglycine: Nature edits synthetic amino acids as well!
- © AK Biokatalyse
Distinct chemical features of fluorinated amino acids may influence synthetic or editing pathways of aminoacyl-tRNA synthetases and contribute to protein quality control. Discrimination (i.e., proofreading) of AARS against artificial ncAAs such as trifluoroethylglycine is highly unlikely in reprogrammed protein biosynthesis since these enzymes have not encountered such a substance during evolution.
- © AK Biokatalyse
Expanding the scope of ribosomal protein synthesis: Nomenclature of the expanded amino acid repertoire (cAAs + ncAAs). Fluorine being not substantially present in the chemistry of living beings is an attractive element in tailoring novel chemical, biophysical, and pharmacokinetic properties of peptides and proteins.
From garlic to genetic code engineering: orthogonal ribosomal protein synthesis with S-Allylcysteine
- © AK Biokatalyse
Design of S-Allylcysteine in Situ Production and Incorporation Based on a Novel Pyrrolysyl-tRNA Synthetase Variant.
The chemical synthesis is still the main source of ncAAs of reprogrammed protein translation. These factors (i.e. market availability, price and purity) represents serious bottlenecks for ncAAs broader application in industrial biotechnology. Therefore, we need broadly applicable with useful chemical handles equipped ncAAs which are intracellularly produced from low-cost chemical precursors added to the growth medium. Here we exemplify these opportunities with our newly engineered PylRS variant capable of activating and tRNA charging with S-allylcysteine (Sac) generated in situ from a cheap precursor allyl mercaptan, using the cysteine biosynthesis pathway. The biological abundance and biosynthetic production pathway of Sac greatly reduces the cost of protein production, potentially making industrial-scale applications feasible.
20899 TGG codons read as thienylpyrrole
The most structurally disturbing deviation introduced into Life so far!
Finally, our evolution experiments have yielded viable cells with a noncanonical genetic code after 506 days of continuous manual culturing, and we have been successfully published! We performed the experimental evolution/adaptation (a so-called long-term cultivation experiment) of the bacterium Escherichia coli, which allowed us the completely replace one of the endogenous building blocks, tryptophan (20899 TGG codons), with an exogenous/synthetic one (thienylpyrrole).
We also received very favorable feedback from our colleagues (Mike Jewett: “Very significant advance!”; Gyorgy Posfai: “It is a significant advance, indeed.”), whereas the pioneer of Xenobiology Philippe Marliere commented “I believe, it is the most structurally disturbing deviation introduced in life so far.”
- © AK Biokatalyse
Original paper in German here. 
Original paper in English here. 
Importance: The chemical composition and the genetic code of an auxotrophic E. coli were changed in the frame of a long-term evolution experiment. During the experiment the cells were gradually forced to replace the natural building block tryptophan with thienopyrrolylalanine in their proteomes. This is the first step in the creation of synthetic life, which should be genetically and metabolically so far away from that found in nature that it cannot survive outside of the laboratory.
Report on the UniCat Cluaster of Excellence Web-page:
Englisch here .
Deutsch here .
A vision of the genetic firewall and synthetic life
- Nediljko Budisa talks about the genetic isolation that can be achieved by recruiting new chemistries in the protoplasma of living cells.
- © Biofaction2014
Ned presented a talk about biocontainment, the genetic firewall, perspectives on synthetic life and artificial biodiversity during the second Bio-Fiction Science Art Film Festival (23 - 25 October, 2014; Museum of Natural History in Vienna, Austria). It was published online by Markus Schmidt and his team at the beginning of this year (Video ). Ned’s talk summarizes ideas, concepts and visions he has developed in the last 10 years, published first in 2011 with Carlos Acevedo-Rocha in Angew. Chem. and more recently in 2014, in Curr.Org.Chem .
Ned believes that the field of genetic code engineering has finally reached intellectual maturity with a clearly defined conceptual framework for future experiments. Recent “Nature” papers of Church (link ) and Isaacs (link ) with further experimental work on biocontainment, via amber stop codons in the frame of synthetic auxotrophy, confirmed his predictions and expectations. In the next stage, the whole field of genetic code engineering should gradually turn to sense-codon reassignment as the most reliable route for changing the genetic code, allowing for the code to be engineered and expanded (link ).
Berlin Golden iGEM-Team
- iGEM goldmedal 2014
- © Copyright??
iGEM 2014: Gold medal for the first and only team in Berlin at the world's largest competition for Synthetic Biology.
iGEM Synthetic Biologie Homepage 
iGEM Team Berlin Homepage 
'Xenobiology meets Astrobiology'
Recently, in collaboration with Dirk
Schulze-Makuch we published two papers regarding the
possible biochemical alternatives for 'terrestial' life
chemistry. In the first paper we elaborated on possibilities for
non-aqueous biochemistry in such seemingly extreme
environments, such as supercritical carbon dioxide (link
). We were driven with recent observations that several bacterial
species are able to toleratet
survive) these conditions.
Surprisingly, our manuscript did not escape attention of the general audience, it is also cited in Wikipedia; see some titles and links below:
“Can life emerge on a planet without water? New theory says yes”
“New Theory Suggests Life Can Emerge On Planets without Water” 
“Alien Life Could Thrive on 'Supercritical' Carbon Dioxide Instead of Water” 
“Philae Probe Latest News: Finds 'Life-Making' Organic Molecules on Comet 67P” 
The second paper, gained surprisingly less attention, although it is to our opinion that this is even more “exotic” that the first one (link ). We tried to make an easy-to-read and informative essay on hypothetical fluorine-based life for a non-specialized readership.
research competition "Jugend forscht"
- Katrina Ying Ma und ihre „Roro Jungs”
- © Copyright??
Students working in synthetic biology supported by
our laboratory won first prize at the annual scientific "Jugend
forscht " competition!
On Wednesday, February 12 2014, the best research projects submitted within the research competition "Jugend forscht" (a German youth science competition) were crowned. Project entitled "Production of synthetic proteins from modified bacteria" which was supported by our co-worker Katrina Ying Ma, received the first price in one of the three Berlin competition centers. Team of the young school level (11th class) young scientists (“Roro boys”; Jonathan Sonntag, Christian Smettan and Nico Stiehl) from the Romain-Rolland-Gymnasium in Berlin-Reinickendorf spent several hours performing experiments with synthetic amino acid incorporation into proteins in our lab. Their project was submitted in the category "Biology" and was subsequently awarded with the first prize in this category at the south competition center. These excellent results come from collaboration between BIG-NSE, Biocatalysis Group and Dr. Angela Köhler-Krützfeldt, teacher at the Romain-Rolland-Gymnasium ("Roro") in the northern part of Berlin.
As we can read from BIG-NSE site (http://www.big-nse.tu-berlin.de ) during the coming weeks, the project will be further optimized before Katrina Ying Ma and her team get submitted it again on the Berlin wide level at the end of March. The winners of this round will get a chance to compete on the nation-wide level. We wish Katrina and her young school level scientists all the best for the next steps of the competition!
Part Three In The Series „Synthetische Biologie im Dialog“ In Marburg, Germany
Ned Budisa discussed in Marburg the social impact of his research in synthetic biology. (German text only )
According to philosopher Prof. Köchy, specialist scientists provide no objective view in current discussion topics, but always seem to bring their personal opinions into the discussion. In Budisa's example, he suggests a chemical concept of life being present, but with also a metaphysical element.
Summary of Ned's Talk: Crucial for "life", however, is not the matter itself, explained Budisa, but the way in which it is organized. This type of organization is defined by the genetic program and its language, the genetic code, is understood by all organisms. "It is perhaps the only language that is not contaminated by culture," says the biochemist. He believes that a modified genetic code in synthetic organisms can also serve as a kind of genetic firewall that prevents the exchange of genetic material between synthetic and natural organisms. In this way, artificial biodiversity could arise, possibly even a parallel world, using previously unused materials... That this could tantamount to a genetic firewall and lead to the establishment of a parallel biological world, had become clear to him only in retrospect.
Broken Bones, Healed Wounds and Engineering of the Genetic Code
Nediljko Budisa explains why we are changing the genetic code and how genetic code engineering, can help us, for example, to create bio-based biomaterials useful in small-bone surgery to close wounds or to knit broken bones together.
- © N. Budisa
Webcast of the talk entitled 'Towards the genetic code with a maximum degree of chemical liberty' given by Nediljko Budisa (Berlin Institute of Technology, Germany) presented at the joint Biochemical Society / Protein Society Focused Meeting 'Protein engineering: new approaches and applications', held in April 2013 (published 09.08.2013).
Tabula Peutingeriana of Synthetic Biology
- © PloSONE
PloSONE published an article entitled "Synthetic Biology: Mapping the Scientific Landscape" (April 2012, Volume 7, Issue 4, e34368) to inform the general audience about the state of the art in the field, including the most important teams, institutions and players. We present here a map that shows the network of authors with five or more publications on synthetic biology in Web of Science.
What is life?
For all those rather interested in general than in particular, Nediljko Budisa wrote an article/book chapter entitled A BRIEF HISTORY OF "LIFE-SYNTHESIS" [German title: Eine kurze Geschichte der „Lebensherstellung”] for Book WAS IST LEBEN? [WHAT IS LIFE] of Nova Acta Leopoldina Series [Bd. 116, Nr. 394 (2012), Vorträge anlässlich der Jahresversammlung vom 23. bis 25. September 2011 zu Halle (Saale)].
The article published on pages 99-118 of the above mentioned book is available from us as PDF file and contains following chapters:
What is life? - The notion of life in social and natural sciences
A culture-free or value-free definition of life?
Why suddenly ‘life synthesis’?
Biology as science of synthesis
Modern history of the “synthesis of life”
Spontaneous generation of life
Emancipation of synthetic biology by “life synthesis”
Notion of the living cell as a factory or a machine with a genetic program
Cell as self-reproducing fluid state automata
Darwinian evolution as a by-product of the chemical properties of complex self-organized systems?
A step toward a parallel biological world?
- Basic attributes of life / living organisms in the light of the evolutionary history and the fundamental notions of individual vs. population. Organisms can be considered as individual autonomy units and as parts of the population that participate in the
- © AK Biokatalyse
Faculty of 1000: our article has been evaluated
Hoesl, M.G., Budisa, N. (2011).
Expanding and Engineering the Genetic Code in a Single Expression
Experiment. ChemBioChem. 12, 552-555.
I was really impressed by the paper as this study shows that the two unique methods of protein engineering with noncanonical amino acids can be quite easily combined in one single in vivo expression experiment. Nowadays, the reassignment of sense codons allows the global substitution of natural amino acids by noncanonical analogues resulting in proteins that are modified at multiple positions to alter overall protein properties. Additionally, it is possible to use orthogonal aminoacyl-tRNA synthetase pairs to co-translationally incorporate noncanonical amino acids site-specifically in response to stop codons. Budisa and Hoesl used the above mentioned supplementation-based incorporation method (SPI) along with this stop codon suppression strategy (SCS) to express modified model proteins. Aside from the global substitution of natural proline and methionine by 4S-fluoroproline and norleucine, respectively, they site-specifically introduced the aromatic photo-crosslinking amino acid p-benzoyl-phenylalanine. Although this strategy needs to be further optimized, the combination of SPI and SCS in one single experiment represents a very promising and straightforward method to combine different beneficial features of noncanonical amino acids at multiple positions and site-specifically in one single protein (Prof. Andreas Marx, University of Konstanz).
- © AK Biokatalyse
In Vivo Double and Triple Labeling of Proteins Using Synthetic Amino Acids
- © AK Biokatalyse
- Pressemitteilung MPI (in German) 
- Pressemitteilung TU Berlin / unicat 
- Article Angewandte 
The oxidation of Met-residues sets off a fatal structural change in the human prion protein
- Figure 1. Oxidation of methionine residues and conformation of the prion protein.
- © AK Biokatalyse
In spite of the huge amount of literature on prion
proteins available to date little is known about the initial event
leading to its misfolding. The moderately hydrophobic canonical amino
acid methionine usually stabilizes α-helices in proteins. However its
oxidized form, methionine-sulfoxide is hydrophilic and has a higher
preference for β-sheets. If the oxidative stress within the cell is
sufficiently high to oxidize certain methionine side chains within the
prion protein, at least one portion of protein´s α-helices is
converted into β-sheet structures.
- Figure 2. Chemical model to study the nature of ?-helix to ?-sheet conversion in prion protein structure
- © AK Biokatalyse
By expanding the genetic code of the AUG triplet with extremely hydrophobic norleucine and extermely hydrophilic metoxinine it is possible to arrest physiologically and pathologically relevant conformational states of the prion protein. In this way we have a kind of Yin and Yang states reflecting two extreme conditions: One prion that mimics the stable, reduced form and one in which all methionine side chains are oxidized. The norleucine variant resulted in an α-helix richt protein that lacks the in vitro aggregation of the parent protein. In contrast, the methoxinine variant resulted in a β-sheet rich protein with strong aggregation tendency.
These extreme conformational states are usually not amenable in animal models nor with peptide fragments. This experimental approach might be highly relevant to study neurodegenerative as well as other aging-related diseases (i. e. Alzheimer and Parkinson).
Wolschner, C., Giese, A., Kretzschmar, H., Huber, R., Moroder, L. and Budisa, N. (2009). Design of anti- and pro-aggregation variants to assess the effects of methionine oxidation in human prion protein. Proc. Natl. Acad. Sci. USA. Early Edition (April 2009), DOI: 10.1073/PNAS.0902688106.
- Pressemitteilung LMU (german) 
- PNAS article 
- Pressemitteilung MPI (german) 
- © AK Biokatalyse
Our long-term goal is the in vivo expression of intrinsically colored proteins without the need for further posttranslational modification or chemical functionalization by externally added reagents. Biocompatible azaindoles/azatryptophans as optical probes represent almost ideal isosteric substitues for natural tryptophan in cellular proteins. To overcome the limits of the traditionally used 7-azaindole/7-azatryptophan, we have substituted the single tryptophan residue in human annexin A5 by 4- and 5-azatryptophan in Trp-auxotropic Escherichia coli cells. Both cells and proteins with these fluorophores possess intrinsic blue fluorescence detectable upon routine UV irradiations. We identified 4-azaindole as a superior optical probe due to its pronounced Stokes-shift of ~130 nm, its significantly higher quantum yield in aqueous buffers and its enhanced quencingresistance. 4-Azaindoles´s intracellular metabolic transformation into 4-azatryptophan coupled with high yield incorporation into proteins is the most straightforward method for the conversion of naturally colorless proteins and cells into their blue counterparts from amino acid precursors.
Lephtien, S., Hoesl, M. G., Merkel, L. and Budisa, N. (2008). Azatryptophans endow proteins with intrinsic blue fluorescence. Proc. Natl. Acad. Sci. USA.[epub ahead of print].
- Article links