Microorganisms will be for sure the first living beings on which we will achieve understanding, both as biological systems and on the details of the functional architecture of their macromolecular components. Microbiology is thus now a focal point of convergence for Physics, Chemistry, Nanosciences and Mathematical modelling.
Our group approaches, from multidisciplinary perspectives, objectives belonging to the emergent field of Synthetic Biology: the generation in microorganisms of non-natural models of amyloid proteinopathies, as useful shortcuts to neurodegenerative diseases. The aim is to later deconstruct their underlying complex core mechanisms. With such purpose, we started from the knowledge acquired (see research line 1) on the conformational changes experienced by ´winged-helix´ (WH) domains upon binding to DNA, as a mechanism enabling initiation of DNA replication of bacterial plasmids (RepA protein), or yeast chromosomes (ORC). RepA protein, upon origin firing, is driven to aggregation through its WH1 domain, constituting a mechanism for negative control of DNA replication.
Through engineering the molecular determinants of RepA-WH1 aggregation (see research line 2), we have built an amyloidogenic device in which fibril assembly in vitro is promoted by interaction with DNA. In the bacterium Escherichia coli, RepA-WH1 is a prion-like protein (prionoid) that generates a vertically transmissible (from mother to daughter cells) amyloid proteinopathy, modulated by an Hsp70 chaperone. RepA-WH1 is bio-safe, since it is not infectious (i.e., not horizontally transmissible) and there is no human protein with a significant degree of sequence similarity. Starting from this synthetic device, we are interested, as biotechnological goals, in the development of new tools for intervening on protein amyloidosis, such as sensors and inhibitor molecules.
MORE INFO: see ´RESEARCH LINES´ below
Molina-García L, Giraldo R . Enabling stop codon read-through translation in bacteria as a probe for amyloid aggregation. Sci Rep 7: 11908.
Molina-García L, Moreno-del Álamo M, Botias P, Martín-Moldes Z, Fernández M, Sánchez-Gorostiaga A, Alonso-del Valle A, Nogales J, García-Cantalejo J, Giraldo R . Outlining core pathways of amyloid toxicity in bacteria with the RepA-WH1 prionoid. Front Microbiol. 8: 539.
Fernández C, González-Rubio G, Langer J, Tardajos G, Liz-Marzán LM, Giraldo R*, Guerrero-Martínez A* . Nucleation of amyloid oligomers by RepA-WH1 prionoid-functionalized gold nanorods. Angew Chem Int Ed. 55: 11237-11241
Molina-García L, Gasset-Rosa F, Moreno-del Álamo M, Fernández-Tresguerres ME, Moreno-Díaz de la Espina S, Lurz R, Giraldo R . Functional amyloids as inhibitors of plasmid DNA replication. Sci Rep 6: 25425
Fernández C, Núñez-Ramírez R, Jiménez M, Rivas G, Giraldo R . RepA-WH1, the agent of an amyloid proteinopathy in bacteria, builds oligomeric pores through lipid vesicles. Sci Rep 6: 23144
Moreno-del Álamo M, Moreno-Díaz de la Espina S, Fernández-Tresguerres ME, Giraldo R . Pre-amyloid oligomers of the proteotoxic RepA-WH1 prionoid assemble at the bacterial nucleoid. Sci Rep 5: 14669
Gasset-Rosa F, Giraldo R . Engineered bacterial hydrophobic oligopeptide repeats in a synthetic yeast prion, [REP-PSI+]. Front Microbiol 6: 311
Torreira E, Moreno-del Álamo M, Fuentes-Perez ME, Fernández C, Martín-Benito J, Moreno-Herrero F, Giraldo R*, Llorca O* . Amyloidogenesis of bacterial prionoid RepA-WH1 recapitulates dimer to monomer transitions of RepA in DNA replication initiation. Structure 23: 183-189
Gasset-Rosa F, Coquel AS, Moreno-del Álamo M, Chen P, Song X, Serrano AM, Fernández-Tresguerres ME, Moreno-Díaz de la Espina S, Lindner AB, Giraldo R . Direct assessment in bacteria of prionoid propagation and phenotype selection by Hsp70 chaperone. Mol Microbiol 91: 1070-1087
Giraldo R . Defined DNA sequences promote the assembly of a bacterial protein into distinct amyloid nanostructures. Proc Natl Acad Sci USA 104: 17388-17393
Giraldo R, Fernández-Tornero C, Evans PR, Díaz-Orejas R, Romero A . A conformational switch between transcriptional repression and replication initiation in the RepA dimerization domain. Nature Struct Biol 10: 565-571
Giraldo R, Díaz-Orejas R . Similarities between the DNA replication initiators of Gram-negative bacteria plasmids (RepA) and eukaryotes (Orc4p) / archaea (Cdc6p). Proc Natl Acad Sci USA 98: 4938-4943
- Deconstructing amyloid proteinopathies in bacterial communities and human cell cultures through Synthetic Biology (BIO2015-68730-R).
- Untangling amyloid proteinopathies and rewiring epigenetics in microorganisms through Synthetic Biology (BIO2012-30852).
- PRODESTECH: From protein structure and dynamics to tailored enzymes, therapeutics, and synthetic macromolecular devices (CSD2009-00088).
- Synthetic replicative and amyloid modules built on microbial WH switch devices (BIO2009-06952).
- Bioinformatics integrative platform for structure-based drug discovery (BIPEDD-CM). Program for collaborative R&D activities in Biosciences in Madrid (P-BIO-0214-2006). http://www.bipedd.es/
- Replicative macromolecular assemblies: Interactions among components and new amyloid nano-structures (BFU2006-00494/BMC).
- Development of new genomic and proteomic tools for the study of the assembly of macromolecular complexes (CAM, GR/SAL/0651/2004).
- Conformational activation and assembly of DNA replication initiation complexes (MCyT-PGC, BMC2003-00088).
- Molecular and Structural Biology of DNA replication initiators in Gram-negative bacteria and yeast (MCyT-PGC, PM99-0096).
Former group members:
- Marta Lages-Gonzalo (MSc student: 1998-1999)
- Teresa Díaz-López (PhD student: 1999-2004)
- Cristina Dávila-Fajardo (PhD student: 2001-2006)
- Alicia Sánchez-Gorostiaga (Postdoc: 2003-2005)
- Asier Jayo-Andrés (Postdoc: 2009)
- M. Elena Fernández-Tresguerres (Staff Sci.: 1972-2013)
- Fátima Gasset-Rosa (MSc/PhD student: 2005-2012 / Postdoc: 2013)
- Ana M. Serrano-López (Technician: 1983-2014)
- María Moreno-del Álamo (MSc/PhD student: 2004-2008 / Postdoc: 2009-2015)
- M.Cruz Sánchez-Martínez (Technician: 2014-2015)
- Laura Molina-García (MSc/PhD student: 2009-2015 / Postdoc: 2015)
- Lucía Sainz-Escudero (Graduate student: 2016)
- Aída Alonso-del Valle (MSc student: 2015-2016)
- Cristina Déniz-Henríquez (MSc student: 2017)