Biotechnology and genetics of extreme thermophiles
Research summary:
Our group uses thermophiles as models for the study of ancestral biological processes and as source of thermostable enzymes and selection platforms for the development of new tools for biotechnological applications. Our main laboratory model is Thermus thermophilus an extreme thermophilic bacterium that is easy to grow under laboratory conditions and amenable to genetic manipulation due to the presence of a highly efficient natural competence apparatus (NCA).
The main biological topics under study in our group during the last years are, mechanisms of horizontal gene transfer, defense mechanisms against the transfer and genome repair pathways and their reciprocal interactions (Fig. 1). The main defense systems we are currently studying are the Argonaute programmable nuclease, the DNA primase-polymerase Primpol, and the AddAB complex (equivalent to RecBCD).
The group is also interested in new biotechnological applications derived from the use of thermophiles. A major effort focuses on the discovery of thermostable enzymes and in the isolation of thermostable variants of enzymes that could better respond to the requirements for industrial biocatalysts or in other applications in the field of Molecular Biology, such as gene edition. For this, new multifunctional vectors are being developed which allow a more efficient identification of thermostable enzymes from metagenomic libraries or the thermo-selection of variants of enzymes of biotechnological interest in modified thermophile host strains.
Figure 1: Interplay between DNA entry and defense mechanisms in T. thermophilus. The different defense proteins act preferentially on DNA that enters through determined ways. R/M, restriction-modification. AddAB, helicase-nuclease complex (similar to RecBCD).
| Last name | Name | Laboratory | Ext.* | Professional category | |
|---|---|---|---|---|---|
| Failde Soler | Marta | 108 | 4525 | Titulado Sup.de Actividades Técn. y Profes. GP1 | |
| Mencia Caballero | Mario | 108 | 4664 | mmencia(at)cbm.csic.es | Profesor Titular Universidad, GA |
| Pulido Sanz | Verónica | 108 | 4525 | Titulado Superior Grado de Doctor | |
| Villamayor Arribas | Álvaro | 108 | 4498 | Tco. de Investigación y Laboratorio |
Relevant publications:
- Mencía, M. (2022). Acid digestion and symbiont: Proton sharing at the origin of mitochondriogenesis? BioEssays, 2200136.
- Verdú, C., Pérez-Arnaiz, P., Peropadre, A., Berenguer, J., and Mencía, M. (2022). Deletion of the primase-polymerases encoding gene, located in a mobile element in Thermus thermophilus HB27, leads to loss of function mutation of addAB genes. Front. Microbiol. 13, 1005862.
- García-Quintans, N., Baquedano, I., Blesa, A., Verdú, C., Berenguer, J. y Mencía, M. (2020). A thermostable DNA primase-polymerase from a mobile genetic element involved in defense against environmental DNA. Environ Microbiol 22, 4647-4657.
- Álvarez, B., Mencía, M., de Lorenzo, V. y Fernández, L.A. (2020) In vivo diversification of target genomic sites using processive T7 RNA polymerase-base deaminase fusions blocked by RNA-guided dCas9. Nat Commun 11, 6436-6449.
- Mencía, M. (2020). The archaeal-bacterial lipid divide, could a distinct lateral proton route hold the answer? Biol Direct 15, 7.
- van Nies, P., Westerlaken, I., Blanken, D., Salas, M., Mencía, M. y Danelon, C. (2018) Self-replication of DNA by its encoded proteins in liposome-based synthetic cells. Nat Commun, 9, 1583.
- Baquedano I, Mencía M, Blesa A, Burrus V, and Berenguer J (2020) ICETh1 & ICETh2, two interdependent mobile genetic elements in Thermus thermophilus transjugation. Environmental Microbiology. 22:158-169.
- Verdú C, Sanchez E. Ortega C, Hidalgo A, Berenguer J, Mencía M. 2019. A modular vector toolkit with a tailored set of thermosensors to regulate gene expression in Thermus. ACS Omega. 4: 14626−14632.
- García-Quintans N, Bowden L, Berenguer J and Mencía. 2019. DNA interference by a mesophilic Argonaute protein, CbcAgo. F1000Research 8: 321.
- Blesa A., Baquedano I., Quintáns N.G., Mata C.P., Castón J.R., Berenguer J. 2017. The transjugation machinery of Thermus thermophilus: Identification of TdtA, an ATPase involved in DNA donation. PloS Genetics. 13 (3) e1006669.
- Blesa A., Quintáns N.G., Baquedano I., Mata C.P., Castón J.R., Berenguer J. 2017. Role of archaeal HerA protein in the biology of the bacterium Thermus thermophilus. Genes 8: 130.
- Blesa A, César CE, Averhoff B, Berenguer J. 2015. Noncanonical cell-to-cell DNA transfer in Thermus spp. is insensitive to argonaute-mediated interference. J Bacteriol. 197:138-146.
- Daan C. Swarts, Matthijs M. Jore, Edze R. Westra, Yifan Zhu, Jorijn H. Janssen, Ambrosius P. Snijders, Yanli Wang, Dinshaw J. Patel, José Berenguer, Stan J. J. Brouns, John van der Oost. 2014. DNA-guided DNA interference by a prokaryotic Argonaute. Nature 507: 258-261.
Doctoral theses:
- Mercedes Sánchez Costa (2020) Estudio y desarrollo de nuevas herramientas para la exploración de ambientes extremos. Universidad Autónoma de Madrid. Directores: José Berenguer y Aurelio Hidalgo.
- Ignacio Baquedano Mozos (2019) ICETh1 & ICETh2, two mobile genetic elements coordinated in Thermus thermophilus transjugation. Universidad Autónoma de Madrid. Directores José Berenguer and Mario Mencía.
- Alba Blesa Esteban (2016) Horizontal gene transfer in Thermus thermophilus: mechanisms and barriers. Universidad Autónoma de Madrid. Director: José Berenguer.
- Yamal Al-ramahi González (2013) Ingeniería de proteínas fluorescentes y aplicaciones de localización celular en microorganismos termófilos. Universidad Autónoma de Madrid. Directores: José Berenguer y Aurelio Hidalgo.
- Noé R. Rivera (2013) Termoestabilización de proteínas de interés biológico. Universidad Autónoma de Madrid. Directores: José Berenguer y Aurelio Hidalgo.
- Laura Álvarez Muñoz (2012) Análisis de la respiración de nitrito en Thermus thermophilus. Universidad Autónoma de Madrid. Director: José Berenguer.
Funded projects in the last years:
- PlastBioTerm: A new approach for the sustainable bioconversion of plastic waste into high-value products based on thermophilic microorganisms and enzymatic synthesis. TED2021-130430B-C22 Entity: Spain Government. Period: 01/12/2022 to 31/11/2024. Mario Mencía (IP)
- DANDIFY: New tools derived from DNA transfer and interference systems from thermophilic bacteria. PID2019-109073RB-I00 Entity: Spain Government. Period: 01/07/2020 to 30/6/2023. José Berenguer (IP), Mario Mencía (CoIP).
- INAGOMICS: DNA-DNA interference mediated by the Argonaute protein of Thermus thermophilus and applications in genome edition. BIO2016-77031-R. Period: 01/01/2017 to 30/6/2020. José Berenguer (IP).
