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Microbial deployment of new-to-nature chemistries for refactoring the barriers between living and non-living matter

Deliverables

Outcome of creative/artistic interventions

The history of technological innovations has demonstrated that the early developers hardly could foresee the various ways the technology would be used and implemented later on To open up all possible narratives of the future we want to invite artists in residency to come and learn in our labs about our mission and give them the opportunity to either carry out an artistic interventions or develop some creative new types of applications of the projects technology

Report on stakeholder involvement

For ellaboration of this report we will involve a number of peers and potential users of the technology such as scientists eg conservational biologists chemists biotechnologists geologists maybe even astrobiologists people form industry small medium and large corporations governance regulatory bodies international organisations like IPCC or CBD and representatives from civil society through workshops and interviews to provide a reality check for the proposed technology

Systems-guided catalogue of sites of intervention with agents delivering NTN reactions

A suite of mathematical and computational approaches ranging from phenomenological to mechanistic will be developed for revisiting the principles that govern the function dynamics and evolution of microbial ecosystems and what allows them to accept new members with novel biochemical properties The way towards topdown synthetic ecology will require new algorithms modeldriven analysis tools and gene function annotation

Report on transposon for converting any Gram-negative bacteria in an HFR strain

This will involve a transposon able to mobilize an entire chromosome though conjugation between a donor and a DNAless recipient For this all the mobtra genes involved in conjugal transfer of superpromiscuous plasmid RP4 will be retrieved from their original genetic frame and assembled as an artificial gene cluster in a miniTn5 transposon vector Upon aquisition of such a transposon any strain will acquire the ability of selftransference and therefore will behave as an HFR strain Highfrequency of recombination that will ease the passing of the genomic information among strains with different degrees of NTN reaction evolution

Proposition of containment needs for microbial agents bearing peribolic reactions

Modeling approaches will be adopted to inspect the pluses and minuses of dealing with live —but heavily refactored microbial agents that could propagate through the Biosphere. This will help to determine the needs of containment of the agents at stake. This lower-scale models will help to understand the resilience and optimal yield conditions of designed microorganisms and microbial consortia and create in silico tests of the proposed peribolic reactions.

A merged model of biogeochemical, biological and industrial matter/energy flow in Earth

The concept of Industrial Metabolism traditionally refers in a metaphoric fashion to the physical traffic of material and energy resources through the economic systems as long as similarly to biological metabolism they are processed resulting into goods and waste We wish to go beyond mere metaphores and try to develop actual integrated models of matter and energy flows through the Biosphere and how they could be deliberately or accidentally altered by the introduction at various scales of the NTN reactions entertained in MADONNA and others that could be developed with the same technologies

Detailed report a genetically optimized artificial carboxylase based on evolved Sav isoforms

The reaction conditions that accompany desired carboxylase recations are often different from physiological conditions (defined as pH of approximately 7, aqueous environments, and ambient temperatures) and turnover numbers very low. In order to make such reaction sustainable and to ultimately recruit such reactions into biology, the protein scaffold has to be evolved. Therefore, we will develope an strategy to implement an enzyme engineering trajectory towards a highly efficient Sav-Pd-catalyst for the production of acrylic acid.

Automated generation of metalloenzymes and information capture through a fitness function

We will take the reaction invented chemically (ie CO2 capture with a metalloenzyme) and and run it in the presence of cells using a chemical droplet robot in which the biological system is programmed to generate peptides that can chelate metal ions to generate ArMs that can be symbiotically selected by the system. This links process engineering to the fitness functions and allows the systems to be linked artificially using such a chem-o-biological robot. The link is software and spectroscopy with chemical feedback. The chemicals can acts as mutagens, and also act as selection agents on the peptides expressed.

Summary and impact of public communication activities

Given the fundamental nature of the scope of our project we feel the responsibility to also share this with the general public through a number of science communication formats eg series of short video clips dissemination though web and social media Science Cafe With these formats we do not only aim to inform the public but also to listen to their thoughts and feedback which will be collected consider and eventually be addressed by the project team to alow for a two way communication between science and the public

Responsible innovation. Report of ethics, safety and security tasks

Reconciliation of geochemical, biological and industrial/human induced global cycles will not only provide a sustainable way of producing and consuming, but will inevitably change the characteristic of the three cycles, diffusing and enlarging the limits of human intervention on the planet. In this report we will ask: what rationale (world view) is behind the projects aim and goal, what other rationales co-exist, which solutions do they provide? What are the ethical dimensions of going forward with the project versus continuing with the unsustainable business-as-usual.

Report on a genetically engineered artificial Fischer-Tropschase enzyme for reduction of CO/CO2 and its expression in vivo

Given that biotinfunctionalized catalysts can be anchored into a streptavidin scaffold this deliverable will report how biotinstreptavidin technology can be exploited selected for incorporation of the Fe4S4 cluster into the genetically encoded protein along with details on characterization of the cofactor and in silico docking studies of the Fe4S4cofactorstreptavidin complex

One genetic switch for self-destroying the endogenous DNA upon exposure to a chemical inducer.

The aim here is to have the choice of destroying altogether the genetic material of E coli and P putida while preserving the whole of the biochemical networks For this the genes ungdut will be deleted and replaced by a tightly regulated ung dut bicistronic operon inducible upon exposure of cells to an external effector eg 3 methylbenzoate While the lack of ungdut will make many Ts of the genome being replaced by U residues their abrupt expression will cleave the chromosome at multiple sites thus converting the cells in a sort of chemical vesicle These will be excellent vessels to develop NTN reactions and as recipients of heavily mutated and edited artificial chromosomes

Morbidostat for heterotic computation of (bio)chemical problems

This is about programming evolution by switching between certain combinations of nutrientssubstrates along with a simple deterministic model to compute evolution heterotically This system is an automated continuousculture device that controls substrate concentration to maintain constant growth inhibition The device runs at a certain interval and adds either fresh medium with a high substrate concentration 24dinitrotoluene DNT as the target molecule in our case or without it By giving it pulses of DNT and letting it recover we expect that the ROS produced by faulty reactions by suboptimal dioxygenases will diversify the corresponding DNA sequences until a biochemical solution is found

Genome edited strains of E. coli and P. putida entirely cyborgized for hosting NTN reactions

The genomes of the two bacterial species adopted in this Project (E. colo and Pseudomonas putida) will be [i] erased of instability determinants and other genes encoding functions considered to be irrelevant for the sake of MADONNA and [ii] endowed with new traits to make them withstand the working conditions of the reactions of interest.

Robotic platform for reverse-reading of chemical reactions into DNA

The coding of DNA in the presence of the process will be reverseread into the system This needs us to generate artificial DNA sequences in the presence of the chemistry and also random peptide synthesis We will build a hybrid digital Complementary metaloxidesemiconductor CMOSdriven synthetic chemical platform to write DNA directly taking advantage of the speed and parallelism of CMOS aiming for GHz write rates on a single strand of DNA within a CMOS nanopore assembler and scale up using PCR this is the reverse of nanopore sequencing

Microdroplet-based environmental simulator

This will be based on a fully autonomous chemical robot system that is able to generate random physicochemical inputs in microdroplet scale. The droplet behaviours will then be analysed, and ranked using a fitness function. This process is continued through iterated generations. This allows inspecting how the genotype is modulated through an envirotype to express the phenotype of interest.

Setup of a Project website and Logo

This Deliverable implies the elaboration of an userfriendly webpage for Communication and Dissemination of Projects activities as well as for internal communication among MADONNA members

Data management plan

This will consist of a document specifying the formats to be followed by the partners for storing the data of interest in a joint repository as well as formal languages for description of actions and constructs

An integrated computational frame for merging NTN reactions to extant metabolism

This is about application of complex networks theory to model new metabolic loops brought about by smallscale and largescale peribolism Meso and largescale models of ecosystems incorporating the NTN reactions set by MADONNA will be produced Our ecosystem description incorporates both standard habitats as well as the highenergy fuelpowered counterparts that are defined by large urban centres and industry By incorporating peribolism we will transform these type of wastesink components into new largescale chemical processes thus deeply changing the global dynamics To this goal we will develop a set of mathematical and computational tools that provide a rationale for the expected responses of this global metabolism on different scales

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Publications

High-throughput optimization of recombinant protein production in microfluidic gel beads

Author(s): Napiorkowska, M., Pestalozzi, L., Panke, S., Held, M., & S. Schmitt.
Published in: Small (Weinheim an der Bergstrasse, Germany),, 2020, ISSN 1613-6829
Publisher: John Wiley & Sons
DOI: 10.1002/smll.202005523

Versioning biological cells for trustworthy cell engineering

Author(s): Tellechea-Luzardo, J., Hobbs, L., Velázquez, E., Pelechova E., Woods, S., de Lorenzo, V. and Krasnogor, N.
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-28350-4

Targeted Depletion of Bacteria from Mixed Populations by Programmable Adhesion with Antagonistic Competitor Cells

Author(s): Ting, S.Y., Martinez-Garcia, E., Huang, S., Bertolli, S.K., Kelly, K.A., Cutler, K.J., Su, E.D., Zhi, H., Tang, Q., Radey, M.C., Raffatellu, M., Peterson, S.B., de Lorenzo, V. and Mougous, J.D.
Published in: Cell Host & Microbe, 2020, ISSN 1934-6069
Publisher: Elsevier
DOI: 10.1016/j.chom.2020.05.006

Standardization of inducer-activated broad host range expression modules: Debugging and refactoring an alkane-responsive AlkS/PalkB device

Author(s): Arce-Rodríguez, A., Benedetti I., Borrero-de Acuña, J.M., Silva-Rocha, R., de Lorenzo, V.
Published in: Synthetic Biology, 23977000, 2021, ISSN 2397-7000
Publisher: Oxford University Press
DOI: 10.1093/synbio/ysab030

Ecological mechanisms underlying aridity thresholds in global drylands

Author(s): Berdugo, M., Vidiella, B., Solé, R.V. and Maestre, F.T.
Published in: Functional Ecology, 2021, ISSN 1365-2435
Publisher: British Ecological Society
DOI: 10.1111/1365-2435.13962

Biotransformation of d-xylose to d-xylonate coupled to medium-chain-length polyhydroxyalkanoate production in cellobiose-grown Pseudomonas putida EM42

Author(s): Dvořák, P.; Kováč, Jozef; Lorenzo, Víctor de
Published in: instname:Consejo Superior de Investigaciones Científicas (CSIC), 17517915, 2020, ISSN 1751-7915
Publisher: John Wiley & Sons
DOI: 10.1111/1751-7915.13574

Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping

Author(s): Simon Höllerer, Laetitia Papaxanthos, Anja Cathrin Gumpinger, Katrin Fischer, Christian Beisel, Karsten Borgwardt, Yaakov Benenson, Markus Jeschek
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-17222-4

The Quest for Xenobiotic Enzymes: From New Enzymes for Chemistry to a Novel Chemistry of Life

Author(s): Tobias Vornholt, Markus Jeschek
Published in: ChemBioChem, 21/16, 2020, Page(s) 2241-2249, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202000121

Low CyaA expression and anti-cooperative binding of cAMP to CRP frames the scope of the cognate regulon of Pseudomonas putida

Author(s): Arce-Rodríguez, A., Nikel, P.I., Calles, B., Chavarría, M., Platero R., Krell, T., de Lorenzo, V.
Published in: Environmental Biotechnology, 2021, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15422

Picking the right metaphors for addressing microbial systems: economic theory helps understanding biological complexity

Author(s): Kim, J., Silva-Rocha, R. and de Lorenzo, V.
Published in: International Microbiology, 2021, ISSN 1139-6709
Publisher: Sociedad Espanola de Microbiologia
DOI: 10.1007/s10123-021-00194-w

Xenobiology: A Journey towards Parallel Life Forms

Author(s): Nediljko Budisa, Vladimir Kubyshkin, Markus Schmidt
Published in: ChemBioChem, 21/16, 2020, Page(s) 2228-2231, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202000141

Missing Links Between Gene Function and Physiology in Genomics

Author(s): Collado-Vides, J., Gaudet, P and de Lorenzo, V.
Published in: Frontiers in Physiology, 2022, ISSN 1664-042X
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2022.815874

Ribonucleases control distinct traits of Pseudomonas putida lifestyle

Author(s): Apura, R., de Lorenzo, V., Arraiano, C.M., Martínez-García, E. and Viegas S.C.
Published in: Environmental Microbiology, 2020, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15291

An automated DIY framework for experimental evolution of Pseudomonas putida

Author(s): Espeso, D.R. Dvořák, P., Aparicio, T. de Lorenzo, V.
Published in: Microbial Biotechnology, 2020, ISSN 1751-7915
Publisher: John Wiley & Sons
DOI: 10.1111/1751-7915.13678

Surface display of designer protein scaffolds on genome-reduced strains of Pseudomonas putida

Author(s): Dvořák, P., Bayer, E.A., de Lorenzo, V.
Published in: ACS Synthetic Biology, 2020, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00276

For the sake of the Bioeconomy: define what a Synthetic Biology

Author(s): de Lorenzo, V., Krasnogor, N., Schmidt, M.
Published in: New Biotechnology, 2020, ISSN 1871-6784
Publisher: Elsevier BV
DOI: 10.1016/j.nbt.2020.08.004

When biology became engineering: Adopting standards for living systems

Author(s): de Lorenzo, V.
Published in: Metode, 2020, ISSN 2174-9221
Publisher: Universidad de Valencia
DOI: 10.7203/metode.11.15975

Concomitant prediction of environmental fate and toxicity of chemical compounds

Author(s): García-Martin, J.A., Chavarría, M., de Lorenzo, V. Pazos, F.
Published in: Biology Methods and Protocols, 2020, ISSN 2396-8923
Publisher: Oxford University Press
DOI: 10.1093/biomethods/bpaa025

Ecological firewalls for synthetic biology

Author(s): Vidiella, B. and Solé, R.
Published in: Iscience, 2022, ISSN 2589-0042
Publisher: Elsevier
DOI: 10.1016/j.isci.2022.104658

Transcriptional control of 2,4-dinitrotoluene degradation in Burkholderia sp. R34 bears a regulatory patch that eases pathway evolution

Author(s): Pérez-Pantoja, D., Nikel, P.I., Chavarría, M. and de Lorenzo, V.
Published in: Environmental Microbiology, 2021, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15472

Engineering Tropism of Pseudomonas putida toward Target Surfaces through Ectopic Display of Recombinant Nanobodies

Author(s): Fraile S., Briones M., Revenga-Parra, M., de Lorenzo V., Lorenzo E. and Martínez-García E
Published in: ACS Synthetic Biology, 2021, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.1c00227

An updated structural model of the A domain of the Pseudomonas putida XylR regulator poses an atypical interplay with aromatic effectors

Author(s): Dvořák, P., Alvarez-Carreño, C., Paradela, A. and de Lorenzo, V.
Published in: Environmental Microbiology, 2021, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15628

Synthetic soil crusts against green-desert transitions: a spatial model

Author(s): Blai Vidiella, Josep Sardanyés, Ricard V. Solé
Published in: Royal Society Open Science, 7/8, 2020, Page(s) 200161, ISSN 2054-5703
Publisher: The Royal Society
DOI: 10.1098/rsos.200161

Contextual dependencies expand the re-usability of genetic inverters

Author(s): Tas, H., Grozinger, L., Stoof, R., de Lorenzo, V, and Goni-Moreno, A.
Published in: NAture Communications, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-20656-5

How To Quantify a Genetic Firewall? A Polarity‐Based Metric for Genetic Code Engineering

Author(s): Schmidt, M. & Kubyshkin, V.
Published in: Chembiochem, 2020, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202000758

The four Fs of the knowledge-based BioEconomy – A homage to Christian Patermann

Author(s): de Lorenzo, V.
Published in: EFB Bioeconomy Journal, 2022, ISSN 2667-0410
Publisher: Elsevier
DOI: 10.1016/j.bioeco.2022.100035

Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents

Author(s): Víctor de Lorenzo
Published in: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 2022, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2021.0395

ArsH protects Pseudomonas putida from oxidative damage caused by exposure to arsenic

Author(s): Páez-Espino, A.D., Nikel, P., Chavarría, M., de Lorenzo, V.
Published in: Environmental Microbiology, 2020, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14991

Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress

Author(s): Nikel, P.I., Fuhrer, T., Chavarría, M., Sánchez-Pascuala, A., Sauer, U. and de Lorenzo, V.
Published in: ISME Journal, 2020, ISSN 1751-7362
Publisher: Nature Publishing Group
DOI: 10.1038/s41396-020-00884-9

ssDNA recombineering boosts in vivo evolution of nanobodies displayed on bacterial surfaces

Author(s): Al-ramahi, Y., Nyerges, A., Margolles, Y., Cerdán, L., Ferenc G., Pál, C., Fernández, L.A. and de Lorenzo, V.
Published in: Communications Biology, 2021, ISSN 2399-3642
Publisher: Nature Communications
DOI: 10.1038/s42003-021-02702-0

Systematic Engineering of Artificial Metalloenzymes for New-to-Nature Reactions

Author(s): T. Vornholt, F. Christoffel, M. M. Pellizzoni, S. Panke, T. R. Ward, M. Jeschek
Published in: Science Advances, 2022, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abe4208

The Wsp intermembrane complex mediates metabolic control of the swim‐attach decision of Pseudomonas putida

Author(s): Ángeles Hueso‐Gil, Belén Calles, Víctor Lorenzo
Published in: Environmental Microbiology, 22/8, 2020, Page(s) 3535-3547, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15126

In vivo diversification of target genomic sites using processive base deaminase fusions blocked by dCas9

Author(s): Álvarez, B., Mencía, M., de Lorenzo, V., Fernández, LA.
Published in: Nature Communications, 20411723, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-20230-z

A Standardized Inverter Package Borne by Broad Host Range Plasmids for Genetic Circuit Design in Gram-Negative Bacteria

Author(s): Tas, H., Goni-Moreno, A. and de Lorenzo, V.
Published in: ACS Synthetic Biology, 2020, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00529

Systematic Engineering of Artificial Metalloenzymes for New-to-Nature Reactions

Author(s): Tobias Vornholt; Fadri Christoffel; Michela M. Pellizzoni; Sven Panke; Thomas R. Ward; Markus Jeschek
Published in: SCIENCE ADVANCES, 23752548, 2021, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.3929/ethz-b-000467617

Hypermutation of specific genomic loci of Pseudomonas putida for continuous evolution of target genes

Author(s): Velázquez, E., Álvarez, B., Fernández, L.A. and de Lorenzo, V.
Published in: Microbial Biotechnology, 2022, ISSN 1751-7915
Publisher: John Wiley & Sons
DOI: 10.1111/1751-7915.14098

Network-level containment of single-species bioengineering

Author(s): Maull, V. and Solé, R.,
Published in: Philosophical Transactions of the Royal Society B,, 2022, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2021.0396

Evolutionary tinkering vs. rational engineering in the times of synthetic biology

Author(s): Víctor de Lorenzo
Published in: Life Sciences, Society and Policy, 14/1, 2018, ISSN 2195-7819
Publisher: Springer
DOI: 10.1186/s40504-018-0086-x

A Post-translational Metabolic Switch Enables Complete Decoupling of Bacterial Growth from Biopolymer Production in Engineered Escherichia coli

Author(s): Gonzalo Durante-Rodríguez, Víctor de Lorenzo, Pablo I. Nikel
Published in: ACS Synthetic Biology, 7/11, 2018, Page(s) 2686-2697, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.8b00345

The Metabolic Redox Regime of Pseudomonas putida Tunes Its Evolvability toward Novel Xenobiotic Substrates

Author(s): Özlem Akkaya, Danilo R. Pérez-Pantoja, Belén Calles, Pablo I. Nikel, Víctor de Lorenzo
Published in: mBio, 9/4, 2018, ISSN 2150-7511
Publisher: ASM
DOI: 10.1128/mbio.01512-18

Improved Thermotolerance of Genome-Reduced Pseudomonas putida EM42 Enables Effective Functioning of the P L / c I857 System

Author(s): Tomás Aparicio, Víctor de Lorenzo, Esteban Martínez-García
Published in: Biotechnology Journal, 14/1, 2019, Page(s) 1800483, ISSN 1860-6768
Publisher: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/biot.201800483

Evolving metabolism of 2,4-dinitrotoluene triggers SOS-independent diversification of host cells

Author(s): Özlem Akkaya, Pablo I. Nikel, Danilo Pérez-Pantoja, Víctor de Lorenzo
Published in: Environmental Microbiology, 21/1, 2019, Page(s) 314-326, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14459

Population dynamics of synthetic terraformation motifs

Author(s): Ricard V. Solé, Raúl Montañez, Salva Duran-Nebreda, Daniel Rodriguez-Amor, Blai Vidiella, Josep Sardanyés
Published in: Royal Society Open Science, 5/7, 2018, Page(s) 180121, ISSN 2054-5703
Publisher: Royal Society
DOI: 10.1098/rsos.180121

The imbroglio of the physiological Cra effector clarified at last

Author(s): Max Chavarría, Víctor de Lorenzo
Published in: Molecular Microbiology, 109/3, 2018, Page(s) 273-277, ISSN 0950-382X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/mmi.14080

Refactoring the upper sugar metabolism of Pseudomonas putida for co-utilization of cellobiose, xylose, and glucose

Author(s): Pavel Dvořák, Víctor de Lorenzo
Published in: Metabolic Engineering, 48, 2018, Page(s) 94-108, ISSN 1096-7176
Publisher: Academic Press
DOI: 10.1016/j.ymben.2018.05.019

Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism

Author(s): Pablo I. Nikel, Víctor de Lorenzo
Published in: Metabolic Engineering, 50, 2018, Page(s) 142-155, ISSN 1096-7176
Publisher: Academic Press
DOI: 10.1016/j.ymben.2018.05.005

Exploiting delayed transitions to sustain semiarid ecosystems after catastrophic shifts

Author(s): Blai Vidiella, Josep Sardanyés, Ricard Solé
Published in: Journal of The Royal Society Interface, 15/143, 2018, Page(s) 20180083, ISSN 1742-5689
Publisher: The Royal Society
DOI: 10.1098/rsif.2018.0083

CRISPR /Cas9‐enhanced ss DNA recombineering for Pseudomonas putida

Author(s): Tomás Aparicio, Víctor Lorenzo, Esteban Martínez‐García
Published in: Microbial Biotechnology, 12/5, 2019, Page(s) 1076-1089, ISSN 1751-7915
Publisher: John Wiley & Sons
DOI: 10.1111/1751-7915.13453

SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts

Author(s): Esteban Martínez-García, Angel Goñi-Moreno, Bryan Bartley, James McLaughlin, Lucas Sánchez-Sampedro, Héctor Pascual del Pozo, Clara Prieto Hernández, Ada Serena Marletta, Davide De Lucrezia, Guzmán Sánchez-Fernández, Sofía Fraile, Víctor de Lorenzo
Published in: Nucleic Acids Research, 48/D1, 2019, Page(s) D1164-D1170, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz1024

Gross transcriptomic analysis of Pseudomonas putida for diagnosing environmental shifts

Author(s): Ángeles Hueso‐Gil, Belén Calles, George A. O'Toole, Víctor Lorenzo
Published in: Microbial Biotechnology, 13/1, 2020, Page(s) 263-273, ISSN 1751-7915
Publisher: Society for Applied Microbiology
DOI: 10.1111/1751-7915.13404

Assembly of a Custom-made Device to Study Spreading Patterns of Pseudomonas putida Biofilms

Author(s): David Espeso, Esteban Martínez-García, Víctor Lorenzo
Published in: BIO-PROTOCOL, 9/10, 2019, ISSN 2331-8325
Publisher: Bio-Protocol
DOI: 10.21769/bioprotoc.3238

Multiple-Site Diversification of Regulatory Sequences Enables Interspecies Operability of Genetic Devices

Author(s): Angeles Hueso-Gil, Ákos Nyerges, Csaba Pál, Belén Calles, Víctor de Lorenzo
Published in: ACS Synthetic Biology, 9/1, 2019, Page(s) 104-114, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.9b00375

Digitalizing heterologous gene expression in Gram‐negative bacteria with a portable ON/OFF module

Author(s): Belén Calles, Ángel Goñi‐Moreno, Víctor Lorenzo
Published in: Molecular Systems Biology, 15/12, 2019, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20188777

Mismatch repair hierarchy of Pseudomonas putida revealed by mutagenic ssDNA recombineering of the pyrF gene

Author(s): Tomas Aparicio, Akos Nyerges, István Nagy, Csaba Pal, Esteban Martínez‐García, Víctor Lorenzo
Published in: Environmental Microbiology, 22/1, 2019, Page(s) 45-58, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14814

Synthetic Biology for Terraformation Lessons from Mars, Earth, and the Microbiome

Author(s): Nuria Conde-Pueyo, Blai Vidiella, Josep Sardanyés, Miguel Berdugo, Fernando T. Maestre, Victor de Lorenzo, Ricard Solé
Published in: Life, 10/2, 2020, Page(s) 14, ISSN 2075-1729
Publisher: MDPI
DOI: 10.3390/life10020014

High-Efficiency Multi-site Genomic Editing of Pseudomonas putida through Thermoinducible ssDNA Recombineering

Author(s): Tomas Aparicio, Akos Nyerges, Esteban Martínez-García, Víctor de Lorenzo
Published in: iScience, 23/3, 2020, Page(s) 100946, ISSN 2589-0042
Publisher: Elsevier
DOI: 10.1016/j.isci.2020.100946

Functional implementation of a linear glycolysis for sugar catabolism in Pseudomonas putida

Author(s): Alberto Sánchez-Pascuala, Lorena Fernández-Cabezón, Víctor de Lorenzo, Pablo I. Nikel
Published in: Metabolic Engineering, 54, 2019, Page(s) 200-211, ISSN 1096-7176
Publisher: Academic Press
DOI: 10.1016/j.ymben.2019.04.005

Pseudomonas putida in the quest of programmable chemistry

Author(s): Esteban Martínez-García, Víctor de Lorenzo
Published in: Current Opinion in Biotechnology, 59, 2019, Page(s) 111-121, ISSN 0958-1669
Publisher: Elsevier BV
DOI: 10.1016/j.copbio.2019.03.012

Spatial organization of the gene expression hardware in Pseudomonas putida

Author(s): Juhyun Kim, Angel Goñi‐Moreno, Belén Calles, Víctor de Lorenzo
Published in: Environmental Microbiology, 21/5, 2019, Page(s) 1645-1658, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14544

Targetron-Assisted Delivery of Exogenous DNA Sequences into Pseudomonas putida through CRISPR-Aided Counterselection

Author(s): Velázquez, V., Al-Ramahi, Y., Tellechea-Luzardo, J., Krasnogor, N., de Lorenzo, V.
Published in: ACS Synthetic Biology, 2021, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.1c00199

Exploiting geometric similarity for statistical quantification of fluorescence spatial patterns in bacterial colonies.

Author(s): Espeso D. R., Algar, E., Martínez-García, E., de Lorenzo, V.
Published in: Exploiting geometric similarity for statistical quantification of fluorescence spatial patterns in bacterial colonies, 2020, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-020-3490-1

Quantitative assessment of morphological traits of planktonic bacterial aggregates

Author(s): Espeso, D.R., Martínez-García, E., de Lorenzo, V.
Published in: Water Research, 2020, ISSN 0043-1354
Publisher: Elsevier BV
DOI: 10.1016/j.watres.2020.116468

A metric space for semantic containment: Towards the implementation of genetic firewalls

Author(s): Markus Schmidt
Published in: Biosystems, 185, 2019, Page(s) 104015, ISSN 0303-2647
Publisher: Elsevier BV
DOI: 10.1016/j.biosystems.2019.104015

Automated design and implementation of a NOR gate in Pseudomonas putida

Author(s): Tas, H., Grozinger, L., Goni-Moreno, A., de Lorenzo, V.
Published in: Synthetic Biology, 2021, ISSN 2397-7000
Publisher: Oxford University Press
DOI: 10.1093/synbio/ysab024

A Bifan Motif Shaped by ArsR1, ArsR2, and Their Cognate Promoters Frames Arsenic Tolerance of Pseudomonas putida

Author(s): Durante-Rodríguez, G., Páez-Espino, D and de Lorenzo, V.
Published in: Frontiers in Microbiology, 2021, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2021.641440

Bottlenecks and opportunities for synthetic biology biosafety standards

Author(s): Pei, L., Garfinkel, M. & Schmidt, M.
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-29889-y

Subcellular Architecture of the xyl Gene Expression Flow of the TOL Catabolic Plasmid of Pseudomonas putida mt-2

Author(s): Kim, J., Goñi-Moreno, A., de Lorenzo, V.
Published in: mBio, 2021, ISSN 2150-7511
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.03685-20

The faulty SOS response of Pseudomonas putida KT2440 stems from an inefficient RecA-LexA interplay

Author(s): Akkaya, Ö., Aparicio, T., Perez-Pantoja, D., de Lorenzo, V.
Published in: Environmental Microbiology, 2020, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15384

Global ecosystem thresholds driven by aridity

Author(s): Miguel Berdugo, Manuel Delgado-Baquerizo, Santiago Soliveres, Rocío Hernández-Clemente, Yanchuang Zhao, Juan J. Gaitán, Nicolas Gross, Hugo Saiz, Vincent Maire, Anika Lehmann, Matthias C. Rillig, Ricard V. Solé, Fernando T. Maestre
Published in: Science, 367/6479, 2020, Page(s) 787-790, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aay5958

Refactoring the Conjugation Machinery of Promiscuous Plasmid RP4 into a Device for Conversion of Gram-Negative Isolates to Hfr Strains

Author(s): Silbert, J., de Lorenzo, V. and Aparicio, T.
Published in: ACS Synthetic Biology, 2021, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00611

Environmental Performance of Pseudomonas putida with a Uracylated Genome

Author(s): Algar, E., Al-Ramahi, Y., de Lorenzo, V.  and Martínez-García, E.
Published in: ChemBioChem, 2020, ISSN 1439-7633
Publisher: John Wiley & Sons
DOI: 10.1002/cbic.202000330

Propagation of Recombinant Genes through Complex Microbiomes with Synthetic Mini-RP4 Plasmid Vectors

Author(s): Aparicio, T., Silbert, J., Cepeda, S. and de Lorenzo, V.
Published in: BioDesign Research, 2022, ISSN 2693-1257
Publisher: American Association for the Advancement of Science
DOI: 10.34133/2022/9850305

Ecological complexity and the biosphere: the next 30 years

Author(s): Solé, R. and Levin, S.
Published in: Philosophical Transactions of the Royal Society B,, 2022, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2021.0376

Naked Bacterium: Emerging Properties of a Surfome-Streamlined Pseudomonas putida Strain

Author(s): Martínez-García, E., Fraile, S., Rodríguez-Espeso, R., Vecchietti, D., Bertoni, G., de Lorenzo, V.
Published in: ACS Synthetic Biology, 2020, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00272

Standardization of regulatory nodes for engineering heterologous gene expression: a feasibility study

Author(s): Nikel, P.I., Benedetti, I., Wirth, N.T., de Lorenzo, V. and Calles, B.
Published in: Microbial Biotechnology, 2022, ISSN 1751-7915
Publisher: John Wiley & Sons
DOI: 10.1111/1751-7915.14063

Emergence of Function and Selection from Recursively Programmed Polymerisation Reactions in Mineral Environments

Author(s): Doran, David; Abul-Haija, Yousef M.; Cronin, Leroy
Published in: Angewandte Chemie (International Ed. in English), 1, 2019
Publisher: American Chemical Society (ACS), Chinese Chemical Society, Chemical Society of Japan, German Chemical Society (GDCh) and the Royal Society of Chemistry
DOI: 10.26434/chemrxiv.7712297.v1

Synthetic soil crusts against green-desert transitions: a spatial model

Author(s): Blai Vidiella, Josep Sardanyés, Ricard V. Solé
Published in: bioRxiv, 2019
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/838631

Systematic Engineering of Artificial Metalloenzymes for New-to-Nature Reactions

Author(s): Tobias Vornholt,Fadri Christoffel, Michela M. Pellizzoni, Sven Panke, Thomas R. Ward, Markus Jeschek
Published in: bioRxiv, 2020
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.07.15.204206

High-Efficiency Multi-site Genomic Editing (HEMSE) Made Easy

Author(s): Aparicio, T., de Lorenzo, V., Martínez-García, E.
Published in: Recombineering. Methods in Molecular Biology, 2022, ISBN 978-1-0716-2233-9
Publisher: Springer Nature
DOI: 10.1007/978-1-0716-2233-9_4

Alternative Biofacts – Life as we don’t (yet) know it

Author(s): Markus Schmidt, Nediljko Budisa
Published in: Art as We Don’t Know It, 2020, Page(s) 20-36, ISBN 978-952-60-8823-5
Publisher: Aalto University Press

Genomic Responses of Pseudomonas putida to Aromatic Hydrocarbons

Author(s): Víctor de Lorenzo, Hiren Joshi
Published in: Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation, 2019, Page(s) 1-15, ISBN 978-3-319-44535-9
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-44535-9_25-1