Summary
Overview
Rodrigo Ledesma-Amaro is leading a research group at the interface of synthetic biology and metabolic engineering. His research lab is based in the Department of Bioengineering and the Center for Synthetic Biology and Innovation.
Research Interests
Synthetic Biology
The group is interested in using and developing new synthetic biology tools that allow us to precisely manipulate microbial cells in a reliable, predictable and standardized way. In particular, we are interested in those cutting edge techniques that permit a fine tuning of metabolic pathways.
Metabolic Engineering
The manipulation and optimization of microbial metabolic pathways are the keys for biotechnology and a bio-based economy. The research group is highly interested in hacking metabolism using synthetic biology tools to create new properties and enhanced behaviors in microbial cells. The engineering strategies are not only designed to produce new high-value products or higher amount of pre-existing products but also to facilitate the downstream and upstream parts of the bioprocesses.
Microbial biotechnology and Microbial communities
Microorganisms are important for both industrial bioprocesses and biomedicine (i.e. gut or skin microbiota). The lab is interesting in a wide array of organisms, from yeast (S. cerevisiea and Y. lipolytica), fungus (A. gossypii) and bacteria (E. coli and Acetobacter) to complex microbial consortia (human and industrial microbiota).
Applications in Industrial biotechnology and biomedicine
As a summary the lab is interested in applying the engineered microorganisms using synthetic biology to the production of 1) high-value chemicals and fuels (biodiesel, lipid-derived compounds, food additives, etc) 2) biomaterials for biomedicine and environmental applications (bacterial cellulose) and 3) understanding microbiome and dysbiosis leading to diseases (skin microbiome, wound healing).
Publications
For a complete list of publications visit:
www.rlalab.org
https://www.researchgate.net/profile/Rodrigo_Ledesma-Amaro
https://scholar.google.com/citations?user=kWTPnDIAAAAJ&hl=es
Join the group
If you are a highly motivated researcher/student with knowledge/interest in the researches described above and you are looking to join the group, please email us with your CV and motivation (r.ledesma-amaro@imperial.ac.uk).
Background
Rodrigo Ledesma-Amaro obtained his PhD at the University of Salamanca under the supervision of Prof. Jose Luis Revuelta, the head of the metabolic engineering group. The PhD thesis is about systems metabolic engineering of A. gossypii for the production of vitamins, nucleosides and lipids. It combines modeling, synthetic biology, systems biology and metabolic engineering techniques and it produced numerous research papers and industrial patents (being currently used by BASF). Before that, Rodrigo coursed an MSc in Microbial Biotechnology at the Universidad Autonoma de Madrid and two undergraduate degrees (Biotechnology and Chemical Engineering) at the University of Salamanca. During his PhD, Rodrigo was a visiting researcher at Prof. Jens Nielsen's group at Chalmers University of Technology (Sweden), at Prof. Jean-Marc Nicaud at INRA (France) and at Prof. Kamisaka's group at AIST (Japan).
After the PhD, he moved to France thanks to an Agreenskills Marie Curie Fellowship and he performed his postdoc in the group of Jean-Marc Nicaud. Most of his postdoctoral research work was done in the oleaginous yeast Yarrowia lipolytica. During those years, Rodrigo engineered this organism to 1) produce different compounds (lipids, lipid-derived chemicals, carotenoids, etc), 2) to be able to use low-cost carbon sources such as lignocellulosic materials or starch and 3) to facilitate the recovery of the products by engineering lipid secretion. During the postdoc, Rodrigo has been teaching synthetic biology related subjects at SUP biotech.
In addition, he has experience in organizing international conferences and teaching courses, in editorial activities for several publishing groups and in supervising and evaluating students, projects and researchers. He also has worldwide collaborations in both academia and industry.
Selected Publications
Journal Articles
Peng H, Chen R, Shaw WM, et al., 2023, Modular metabolic engineering and synthetic coculture strategies for the production of aromatic compounds in yeast, Acs Synthetic Biology, Vol:12, ISSN:2161-5063, Pages:1739-1749
Kaur Aulakh S, Sellés Vidal L, J. South E, et al., 2023, Spontaneously established syntrophic yeast communities improve bioproduction, Nature Chemical Biology, Vol:19, ISSN:1552-4450, Pages:951-961
Graham AE, Ledesma-Amaro R, 2023, The microbial food revolution, Nature Communications, Vol:14, ISSN:2041-1723
Coppens L, Tschirhart T, Leary DH, et al., 2023, Vibrio natriegens genome-scale modeling reveals insights into halophilic adaptations and resource allocation, Molecular Systems Biology, Vol:19, ISSN:1744-4292, Pages:1-16
Venturelli OS, Wang HH, Estrela S, et al., 2023, What is the key challenge in engineering microbiomes?, Cell Systems, Vol:14, ISSN:2405-4720, Pages:85-90
Park Y-K, Ledesma-Amaro R, 2023, What makes Yarrowia lipolytica well suited for industry?, Trends in Biotechnology, Vol:41, ISSN:0167-7799, Pages:242-254
Wu Y, Li Y, Jin K, et al., 2023, CRISPR-dCas12a-mediated genetic circuit cascades for multiplexed pathway optimization, Nature Chemical Biology, ISSN:1552-4450
Ledesma Amaro R, Ellis T, Shaw W, et al., 2022, Inducible expression of large gRNA arrays for multiplexed CRISPRai applications, Nature Communications, Vol:13, ISSN:2041-1723
Yu W, Jin K, Wu Y, et al., 2022, A pathway independent multi-modular ordered control system based on thermosensors and CRISPRi improves bioproduction in Bacillus subtilis, Nucleic Acids Research, Vol:50, ISSN:0305-1048, Pages:6587-6600
Xu Y, Wang X, Zhang C, et al., 2022, De novo biosynthesis of rubusoside and rebaudiosides in engineered yeasts, Nature Communications, Vol:13, ISSN:2041-1723
Ledesma Amaro R, Ouldridge T, O'Hare D, et al., 2022, Synthetic biology and bioelectrochemical tools for electrogenetic system engineering, Science Advances, Vol:8, ISSN:2375-2548
Jiang W, Hernández Villamor D, Peng H, et al., 2021, Metabolic engineering strategies to enable microbial utilization of C1 feedstocks, Nature Chemical Biology, Vol:17, ISSN:1552-4450, Pages:845-855
Xu X, Li X, Liu Y, et al., 2020, Pyruvate-responsive genetic circuits for dynamic control of central metabolism, Nature Chemical Biology, Vol:16, ISSN:1552-4450, Pages:1261-1268
McCarty NS, Graham AE, Studená L, et al., 2020, Multiplexed CRISPR technologies for gene editing and transcriptional regulation, Nature Communications, Vol:11, ISSN:2041-1723
Det-Udom R, Gilbert C, Liu L, et al., 2019, Towards semi-synthetic microbial communities: Enhancing soy sauce fermentation properties in B. subtilis co-cultures, Microbial Cell Factories, Vol:18, ISSN:1475-2859
McCarty NS, Shaw WM, Ellis T, et al., 2019, Rapid assembly of gRNA arrays via modular cloning in yeast, Acs Synthetic Biology, Vol:8, ISSN:2161-5063, Pages:906-910
McCarty NS, Ledesma-Amaro R, 2019, Synthetic biology tools to engineer microbial communities for biotechnology, Trends in Biotechnology, Vol:37, ISSN:0167-7799, Pages:181-197
Larroude M, Rossignol T, Nicaud J-M, et al., 2018, Synthetic biology tools for engineering Yarrowia lipolytica, Biotechnology Advances, Vol:36, ISSN:0734-9750, Pages:2150-2164
Blount B, Gowers G, Ho JCH, et al., 2018, Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome, Nature Communications, Vol:9, ISSN:2041-1723
Larroude M, Celinska E, Back A, et al., 2017, A synthetic biology approach to transform Yarrowia lipolytica into a competitive biotechnological producer of β-carotene, Biotechnology and Bioengineering, Vol:115, ISSN:1097-0290, Pages:464-472