Publications

2020

Batianis, C., Kozaeva, E., Damalas, S., Martin Pascual, M., Volke, D., Nikel, P. I. & Martins dos Santos, V. A. P., An expanded CRISPRi toolbox for tunable control of gene expression in Pseudomonas putida. (2020), Microbial Biotechnology. 13, 2, p. 368-385 https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/1751-7915.13533

2019

Demming, Hauer et al., Asymmetirc Enzymatic Hydration of Unactivated, Aliphatic Alkenes, Angew. Chem. Int. Ed., 58 (2019), 173-177. https://doi.org/10.1002/anie.201810005

Kim, J., Goñi-Moreno, A., Calles, B., and de Lorenzo, V. (2019). Spatial organization of the gene expression hardware in Pseudomonas putida. Environ Microbiol (In Press) doi: 10.1111/1462-2920.14544

Pham, Nhung, et al. "Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling." Metabolites 9.2 (2019): 28. https://www.mdpi.com/2218-1989/9/2/28

2018

Akkaya, Ö., Nikel, P.I., Pérez-Pantoja, D. and de Lorenzo, V. (2018) Evolving metabolism of 2,4-dinitrotoluene triggers SOS-independent diversification of host cells. Env Microbiol. 2018 Oct 25. doi: 10.1111/1462-2920.14459.

Akkaya, O., Pérez-Pantoja, D., Calles, B., Nikel, P.I. and de Lorenzo, V. (2018) The metabolic redox regime of Pseudomonas putida tunes its evolvability towards novel xenobiotic substrates. mBio 9: e01512-18-e01512-18

Andrade JM, Dos Santos RF, Chelysheva I, Ignatova Z, and Arraiano CM. (2018). The RNA binding protein Hfq is important for ribosome biogenesis and affects translation fidelity. The EMBO Journal. e97631 https://drive.google.com/file/d/1DM3MUYz7N-fSPMt8THCUoMzH4JAMh8vl/view?usp=sharing

Aparicio, T., de Lorenzo V., Martínez-García, E. (2018) Improvedh termotolerance of genome-reduced Pseudomonas putida EM42 enables effective functioning of the PL/cI857 system. Biotech J. 2018 Nov 14(1):e1800483. doi: 10.1002/biot.201800483

Chavarría, M. and de Lorenzo, V. (2018) The imbroglio of the physiological Cra effector clarified at last. Mol Microbiol. 109(3):273-277. doi: 10.1111/mmi.14080.

de Lorenzo, V. (2018) Biodegradation and Bioremediation: An Introduction. In Handbook of Hydrocarbon and Lipid Microbiology (Ed. K.N. Timmis) Springer-Verlag Berlin Heidelberg. Vol. Consequences of Microbial Interaction with Hydrocarbons, Oils and Lipids: Biodegradation and Bioremediation (In Press).

de Lorenzo, V. (2018) Environmental microbiology to the rescue of planet Earth. Environ Microbiol http://hdl.handle.net/10261/167703

de Lorenzo, V. (2018) Evolutionary tinkering vs. rational engineering in the times of Synthetic Biology. Life Sciences, Society & Policy 14: 18. DOI https://dx.doi.org/10.1186/s40504-018-0086-x

Durante-Rodríguez, G., de Lorenzo, V. and Nikel, P.I. (2018) A post-translational metabolic switch enables complete decoupling of bacterial growth from biopolymer production in engineered Escherichia coli. ACS Synth. Biol., 2018, 7 (11), pp 2686–2697 DOI: 10.1021/acssynbio.8b00345

Dvorak, P. and de Lorenzo, V. (2018). Refactoring the upper sugar metabolism of Pseudomonas putida for co-utilization of cellobiose, xylose, and glucose. Metab Eng. 48: 94-108 48:94-108. doi: 10.1016/j.ymben.2018.05.019

Nikel P.I. and de Lorenzo V (2018) Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism. Metab Eng doi: 10.1016/j.ymben.2018.05.005

Pérez-Pantoja, D., Kim, J., Platero, R. and de Lorenzo, V. (2018) The interplay of EIIANtr with C-source regulation of the Pu promoter of Pseudomonas putida mt-2. Env Microbiol. Sep 13. doi: 10.1111/1462-2920.14410 

Rodríguez Espeso, D., Martínez-García, E., Carpio, A., and de Lorenzo, V. Dynamics of Pseudomonas putida biofilms in an upscale experimental. framework. J Ind Microbiol Biotech. Vol.45(10), p.899-911. DOI: 10.1007/s10295-018-2070-0

Viegas, S.C., Apura, P., Martínez-García, E., de Lorenzo, V. and Arraiano, C.M. (2018) Modulating heterologous gene expression with portable mRNA-stabilizing 5’-UTR sequences. ACS Synth Biol. 7 (9), pp 2177–2188 DOI: 10.1021/acssynbio.8b00191

2017

Bahls, M.O., Kardashliev, T., Panke, S., Novel Sensors for Engineering Microbiology, Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Production of Fuels and Chemicals, Part of the series Handbook of Hydrocarbon and Lipid Microbiology, September 2017, pp 1-27

Demming, R.M., Otte, K.B., Nestl, B.M., Hauer, B., Optimized Reaction Conditions Enable the Hydration of Non-natural Substrates by the Oleate Hydratase from Elizabethkingia meningoseptica, ChemCatChem 2017, 9, 758 – 766 http://doi.wiley.com/10.1002/cctc.201601329

Dvořák P, Nikel PI, Damborský J, de Lorenzo V., Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology. Biotechnol Adv. 2017 Aug 5. pii: S0734-9750(17)30089-7. doi: 10.1016/j.biotechadv.2017.08.001. [Epub ahead of print] Review. PMID:28789939. https://www.ncbi.nlm.nih.gov/pubmed/28789939

Goñi-Moreno Á, Benedetti I, Kim J, de Lorenzo V. Deconvolution of Gene Expression Noise into Spatial Dynamics of Transcription Factor-Promoter Interplay. ACS Synth Biol. 2017 Jul 21;6(7):1359-1369. doi: 10.1021/acssynbio.6b00397. Epub 2017 Apr 17. PMID:28355056. https://www.ncbi.nlm.nih.gov/pubmed/28355056

Jiménez-Díaz, L., Caballero, A., Pérez-Hernández, N., Segura, A., Microbial alkane production for jet fuel industry: motivation, state of the art and perspectives, Microbial Biotechnology 10/1 (2017): 103-124, http://europepmc.org/articles/PMC5270751

Kees C. H. van der Ark, Ruben G. A. van Heck, Vitor A. P. Martins Dos Santos, Clara Belzer, Willem M. de Vos, Microbiome 5/1, 2017, http://europepmc.org/articles/PMC5512848

Kuschel M., Siebler, F. Takors, R. (2017). Lagrangian Trajectories to Predict the Formation of Population Heterogeneity in Large-Scale Bioreactors. Bioengineering 4(27)  https://www.mdpi.com/2306-5354/4/2/27.

de Lorenzo V, Schmidt M. Biological standards for the Knowledge-Based BioEconomy: What is at stake. N Biotechnol. 2017 May 4. pii: S1871-6784(16)32621-8. doi: 10.1016/j.nbt.2017.05.001. [Epub ahead of print] Review.
PMID: 28479235. https://www.ncbi.nlm.nih.gov/pubmed/28479235

Martínez-García E, Aparicio T, de Lorenzo V, Nikel PI (2017) Engineering Gram-negative microbial cell factories using transposon vectors. Methods Mol Biol. 1498: 273-293. DOI: 10.1007/978-1-4939-6472-7_18 http://hdl.handle.net/10261/146960

Nestl, B., Geinitz, Ch., Popa, St., Rizek, S., Haselbeck, R.J., Stephen, R., Noble, M.A., Fischer, M.-Ph., Ralph, E.C., Ting Hau, H., Man, H., Omar, M., Turkenburg, J.P., van Dien, St., Culler, St. J., Grogan, G., Hauer, B. (2017), Structural and functional insights into asymmetric enzymatic dehydration of alkenols, Nature Chemical Biology 13/3: 275-281, http://eprints.whiterose.ac.uk/110413/1/Nestl_accepted_manuscript.doc

Ricaurte DE, Martínez-García E, Nyerges Á, Pál C, de Lorenzo V, Aparicio T.A. (2017) A standardized workflow for surveying recombinases expands bacterial genome-editing capabilities. Microb Biotechnol. doi: 10.1111/1751-7915.12846. https://doi.org/10.1111/1751-7915.12846

Sánchez-Pascuala A, de Lorenzo V, Nikel PI., Refactoring the Embden-Meyerhof-Parnas Pathway as a Whole of Portable GlucoBricks for Implantation of Glycolytic Modules in Gram-Negative Bacteria. ACS Synth Biol. 2017 May 19;6(5):793-805. doi: 10.1021/acssynbio.6b00230. Epub 2017 Feb 9. PMID:28121421. https://www.ncbi.nlm.nih.gov/pubmed/28121421

2016

Aparicio, T., Ingemann, S., Nielsen A., de Lorenzo V. and Martínez-García (2016) The Ssr protein (T1E_1405) from Pseudomonas putida DOT-T1E enables oligonucleotide-based recombineering in platform strain P. putida EM42. Biotechnol J. 11, 1309–1319 http://dx.doi.org/10.1002/biot.201600317

Arce-Rodríguez, A., Calles, B., Nikel, P-I. and de Lorenzo, V. (2016) The RNA chaperone Hfq enables the environmental stress tolerance super-phenotype of Pseudomonas putida. Env Microbiol. 18(10):3309-3326. http://dx.doi.org/10.1111/1462-2920.13052

Belda, E., Heck, R. G.A. van , Lopez-Sanchez, M., Cruveiller, St., Barbe, V., Fraser, C., Klenk, H. P., Petersen, J., Morgat, A., Nikel, P. I. , Vallenet, D., Rouy, Z., Sekowska, A., Martins dos Santos, V. A.P. , de Lorenzo, V., Danchin, The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis. Environmental Microbiology 18 (2016)10.

Benedetti, I., Nikel, P.I. and de Lorenzo, V. (2016) Data on the standardization of a cyclohexanone-responsive expression system for Gram-negative bacteria. Data in Brief. 6(2016)738–744 http://dx.doi.org/10.1016/j.dib.2016.01.022

Espeso, D. R., Martínez-García, E., de Lorenzo, V., Goñi-Moreno, Á., Physical Forces Shape Group Identity of Swimming Pseudomonas putida Cells, Frontiers in Microbiology 7 (2016), http://journal.frontiersin.org/Article/10.3389/fmicb.2016.01437/abstract

van Heck Ruben G. A., Ganter Mathias, Martins dos Santos Vitor A. P., Stelling Joerg, Efficient Reconstruction of Predictive Consensus Metabolic Network Models. August 26, 2016 http://dx.doi.org/10.1371/journal.pcbi.1005085

de las Heras, A., Martinez-Garcia, E., Domingo-Sananes, M.R., Fraile, S. and de Lorenzo, V. (2016) Rationally rewiring the connectivity of the XylR/Pu regulatory node of the m-xylene degradation pathway in Pseudomonas putida Integr Biol. V 8. 571 - 76 http://dx.doi.org/10.1039/c5ib00310e

Kim, J., Pérez-Pantoja, D., Silva-Rocha, R., Oliveros, J.C. and de Lorenzo, V. (2016) High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2. Env Microbiol. 18(10):3327-3341. http://dx.doi.org/10.1111/1462-2920.13054

Koehorsty Jasper J, van Dam Jesse CJ, van Heck Ruben GA, Saccenti Edoardo, Martins dos Santos Vitor AP, Suarez-Diez Maria, Schaap Peter J, Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data. Scientific reports (Accepted, not published). http://library.wur.nl/WebQuery/wurpubs/511217

Koehorst, J.J. , Saccenti, E. , Schaap, P.J. , Martins dos Santos, V.A.P. , Suarez-Diez, M. (2016) Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics. F1000 Research 5 (2016). http://library.wur.nl/WebQuery/wurpubs/509689

de Lorenzo, V., Marlière, P. and Solé, R. (2016) Bioremediation at a global scale: from the test tube to planet Earth. Microb Biotech 9: 618-625 http://dx.doi.org/10.1111/1751-7915.12399

de Lorenzo, V., Systems and Synthetic Biology in Hydrocarbon Microbiology: Tools, Hydrocarbon and Lipid Microbiology Protocols (2016): pp 1-7 http://link.springer.com/10.1007/8623_2015_185

Martínez-García E., Aparicio T., de Lorenzo, V., Nikel PI (2016) Engineering Gram-negative microbial cell factories using transposon vectors. Methods Mol Biol. 1498: 273-293. http://dx.doi.org/10.1007/978-1-4939-6472-7_18

Martínez-García, E. and de Lorenzo, V. (2016) The quest for the minimal bacterial genome. Curr Op Biotechnol 42: 216-224. http://dx.doi.org/10.1016/j.copbio.2016.09.001

Molina, L., Geoffroy, V.A., Segura, A., Udaondo, Z., Ramos, J.-L., Iron Uptake Analysis in a Set of Clinical Isolates of Pseudomonas putida, Frontiers in Microbiology 7 (2016), http://hdl.handle.net/10261/153037

Molina-Santiago C.​, Cordero B., Daddaoua A., Udaondo Z., Manzano J., Valdivia M., Segura A.,, Ramos J., Duque E.(2016) Pseudomonas putida as a platform for the synthesis of aromatic compounds. Microbiol (2016) 9, https://doi.org/10.1099/mic.0.000333

Nikel, P.I., Pérez-Pantoja and de Lorenzo, V. (2016) Pyridine nucleotide transhydrogenases enable redox balance of Pseudomonas putida during biodegradation of aromatic compounds. Environ Microbiol.(2016) 6, http://dx.doi.org/10.1111/1462-2920.13434

Rodriguez-Espeso, D., Martínez García, E., de Lorenzo, V. and Goñi-Moreno (2016) Physical forces shape group identity of swimming Pseudomonas putida cells. Front Microbiol 7: 1437. http://dx.doi.org/10.3389/fmicb.2016.01437

Saramago, M., Peregrina, A., Robledo, M., Matos, R.G., Hilker, R., Serrania, J., Becker, A., Arraiano, C.M., Jiménez-Zurdo, J.I., Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation, Nucleic Acids Research 45/3 (2016): 1371-1391, http://europepmc.org/articles/PMC5388416

Schmidt M. and de Lorenzo, V. (2016). Synthetic bugs on the loose: containment options for deeply engineered (micro)organisms. Curr Op Biotechnol. Volume 38, April 01, 2016, Pages 90-96  http://dx.doi.org/10.1016/j.copbio.2016.01.006

Pseudomonas putida as a platform for the synthesis of aromatic compounds Free