CENTRO DE BIOLOGÍA MOLECULAR SEVERO OCHOACaptura de pantalla 2022 09 14 a las 10.27.10    

Ultrahigh-throughput discovery and engineering of enzymes for biotechnological applications

Research summary:

Microbial diversity is a vast reservoir of genetic information that can be valorized through industrial application, from biosynthetic gene clusters to novel protein catalysts. The synergy between new experimental discovery tools based on biology and those based on nanotechnologies are instrumental to find relevant genes faster and more efficiently, enabling especially academic labs to undertake screening campaigns until now costly and limited to large enterprises.

En nuestro laboratorio utilizamos selecciones biológicas o métodos de cribado de ultra-alta capacidad basados en microfluídica para encontrar genes y enzimas de interés en la diversidad natural o artificial. Las selecciones biológicas acoplan la mejora en una propiedad de interés a la supervivencia de un huésped bajo presión de selección. Utilizando este y otros métodos de ingeniería de proteínas hemos desarrollado variantes estables y solubles de enzimas para biocatálisis, como esterasas, deshalogenasas, además de proteínas fluorescentes para aplicaciones de localización in vivo a altas temperaturas.

However, the complexity of cellular metabolism limits the application of biological selections. Microfluidics enables the miniaturization of assays with throughput of kHz and a 1000x reduction in volume and costs. Therefore, droplet microfluidics achieves throughputs typical of biological selections with none of their complexity. Within the H2020 project MetaFluidics, in our laboratory, we have implemented a fluorescence-based microfluidic sorting platform and assays to find stable hydrolases in thermal environments as well as other relevant enzymes for biocatalysis. This has entailed developing news hosts and methods for functional expression, compatible with enzymatic assays at high temperatures.


Ultrahigh-thropughput screening using droplet microfluidicsA) Growth of microorganisms and cells in droplets after 24 h incubation. B) Ultrahigh-throughput screening of thermozymes using Thermus thermophilus as host. C) In vitro transcription translation (IVVTT) using T. thermophilus cell-free extracts. D) Digital PCR to detect rare microbes (mcirobial dark matter) and genes). Images by M. Almendros, A. Lopes and M. Sánchez


* For external calls please dial 34 91196 followed by the extension number
Last nameNameLaboratoryExt.*e-mailProfessional category
Blas MuñozLaura1084525laura.blas(at)cbm.csic.esTitulado Sup.de Actividades Técn. y Profes. GP1
Bosch ReñeSandra1084525sbosch(at)cbm.csic.esTitulado Superior Grado de Doctor
Cecchini Davide Agostino1084525davide.cecchini(at)uam.esInvestigador Doctor
Hidalgo HuertasAurelio1084527ahidalgo(at)cbm.csic.esProfesor Titular Universidad, GA
Lorente ArévaloÁlvaro1084525alorente(at)cbm.csic.esTitulado Sup.de Actividades Técn. y Profes. GP1
Margot Léa1084524Titulado Sup.de Actividades Técn. y Profes. GP1
Martínez SalvadorJohn108/1274525/4569john.martinez(at)cbm.csic.esTco. de Investigación y Laboratorio
Nejda HamdounNargisse1084524n.nejda(at)cbm.csic.esTitulado Sup.de Actividades Técn. y Profes. GP1
Ortega PlazaCarmen1084525cortega(at)cbm.csic.esTco. de Investigación y Laboratorio
Palacios AzconaAitor1084525Estudiante TFG
Pérez ArnaizPatricia1084498pparnaiz(at)cbm.csic.esProfesor Ayudante Doctor Universidad
Saiz AlvarezLaura Pilar1084525Titulado Sup.de Actividades Técn. y Profes. GP1

Relevant publications:

  • Mate DM, Rivera NR, Sanchez-Freire E, Ayala JA, Berenguer J and Hidalgo A (2019) Thermostability enhancement of the Pseudomonas fluorescens esterase I by in vivo folding selection in Thermus thermophilus. Biotech. Bioeng. doi: 10.1002/bit.27170
  • Verdú C, Sanchez-Freire E, Ortega C, Hidalgo A, Berenguer J* and Mencía M* (2019) A modular vector toolkit with a tailored set of thermosensors to regulate gene expression in Thermus thermophilus. ACS Omega doi: 10.1021/acsomega.9b02107
  • Castillo J, Caminata Landriel S, Sánchez Costa M, Taboga OA, Berenguer J, Hidalgo A, Ferrarotti SA, Costa H (2018) A single mutation in cyclodextrin glycosyltransferase from Paenibacillus barengoltzii changes cyclodextrin and maltooligosaccharides production. Protein Eng. Des. Sel. 31: 399-407. doi. 10.1093/protein/gzy034
  • Consolati T, Bolívar JM, Petrasek Z, Berenguer J, Hidalgo A, Guisán JM, and Nidetzky B (2018) Bio-based pH internally sensitive materials: immobilized yellow fluorescent protein as optical sensor for spatiotemporal mapping of pH inside porous matrices. ACS Appl. Mater. Inter. 10: 6858-6868. doi: 10.1021/acsami.7b16639
  • Ribeiro AL, Mencía M and Hidalgo A (2018) A brief guide to the high-throughput expression of directed evolution libraries. Methods Mol. Biol. 1685: 131-143. doi: 10.1007/978-1-4939-7366-8_7
  • Ribeiro AL, Sánchez M, Hidalgo A, and Berenguer J (2017) Stabilization of enzymes by using thermophiles. Methods Mol. Biol. 1465: 297-312. doi: 10.1007/978-1-4939-7183-1_21
  • Berenguer J, Mencía M, and Hidalgo A (2017) Are in vivo selections on the path to extinction? Microb. Biotechnol. 10: 46-49. doi: 10.1111/1751-7915.12490
  • Vettone A, Serpe M, Hidalgo A, Berenguer J, Del Monaco G, Valenti A, Rossi M, Ciaramella M and Perugino G (2016) A novel thermostable protein-tag: optimization of the Sulfolobus solfataricus DNA-alkyl-transferase by protein engineering. Extremophiles 2016, 20: 1-13. Doi: 10.1007/s00792-015-0791-9
  • Hidalgo A, Schließmann A and Bornscheuer UT (2014) One-pot Simple methodology for CAssette Randomization and Recombination for focused directed evolution (OSCARR). Methods. Mol. Biol. 1179: 207-212. doi: 10.1007/978-1-4939-1053-3_14
  • Hidalgo A and Berenguer J (2013) Biotechnological applications of Thermus thermophilus as host. Curr. Biotechnol. 2: 304-312. doi: 10.2174/18722083113076660030
  • Torres LL, Cantero A, Del Valle M, Marina A, Lopez-Gallego F, Guisan JM, Berenguer J and Hidalgo A (2013) Engineering the substrate specificity of a thermophilic penicillin acylase from Thermus thermophilus. Appl. Environ. Microbiol. 79: 1555-1562. doi: 10.1128/AEM.03215-12
  • Torres LL, Ferreras ER, Cantero A, Hidalgo A and Berenguer J (2012) Functional expression of a penicillin acylase from the extreme thermophile Thermus thermophilus HB27 in Escherichia coli. Microb. Cell Fact. 11: 105. doi: 10.1186/1475-2859-11-105.
  • Torres LLSchließmann ASchmidt MSilva-Martin NHermoso JABerenguer JBornscheuer UT and Hidalgo A (2012) Promiscuous enantioselective (-)-γ-lactamase activity in the Pseudomonas fluorescens esterase I. Org. Biomol. Chem. 10: 3388-3392. doi:

Last doctoral theses:

  • Yamal Al-ramahi González (2013) Fluorescent protein engineering and applications in thermophile microorganisms. Universidad Autónoma de Madrid. Supervisors: Aurelio Hidalgo y José Berenguer.
  • Noé R. Rivera (2013) Thermal stabilization of biotechnologically relevant proteins. Universidad Autónoma de Madrid. Supervisors: Aurelio Hidalgo y José Berenguer.

Ongoing doctoral theses:

  • Mercedes Sánchez Costa. Discovery and characterization of thermostable enzymes for biocatalysis. Supervisors: Aurelio Hidalgo y José Berenguer.
  • Sandra Bosch Reñé. Selection of thermostable biocatalysts for green chemistry using thermophile microorganisms. Supervisor: Aurelio Hidalgo.
  • Jorge Bravo Villanueva. Ultrahigh-throughput screening methods based on components from thermophile microorganisms. Supervisor: Aurelio Hidalgo.


  • Desarrollo de sistemas para la selección de proteínas termoestables mediante expresión in vivo e in vitro a alta temperatura. Entidad financiadora: UAM. UAM/89. Período: 01/02/2017-31/12/2021. Tipo de participación: IP.
  • Advanced toolbox for rapid and cost-effective functional metagenomic screening: microbiology meets microfluidics (METAFLUIDICS). Entidad financiadora: Unión Europea H2020. GA 685474. Período: 01/06/2016-30/05/2020. Tipo de participación: Coordinación.
  • Sustainable industrial processes based on a C-C bond-forming enzyme platform (CarbaZymes). Entidad financiadora: Unión Europea H2020. GA 635595. Período: 01/04/2015-31/03/2019. Tipo de participación: Socio.
  • Ultrahigh-throughput platform for the screening of thermostable proteins by thermophilic in vitro transcription-translation and microfluidics (HOTDROPS). Entidad financiadora: Unión Europea FP7. GA 324439. Período: 01/06/2013-30/05/2017. Tipo de participación: Socio.
  • Selección de alta eficiencia de biocatalizadores termoestables para química verde empleando microorganismos termófilos modificados. Entidad financiadora: Ministerio de Economía y Competitividad. Período: 01/01/2013-31/12/2016. Tipo de participación: Co-IP.

NOTE! This site uses cookies and similar technologies.

If you not change browser settings, you agree to it. Learn more

I understand


What are cookies?

A cookie is a file that is downloaded to your computer when you access certain web pages. Cookies allow a web page, among other things, to store and retrieve information about the browsing habits of a user or their equipment and, depending on the information they contain and the way they use their equipment, they can be used to recognize the user.

Types of cookies

Classification of cookies is made according to a series of categories. However, it is necessary to take into account that the same cookie can be included in more than one category.

  1. Cookies according to the entity that manages them

    Depending on the entity that manages the computer or domain from which the cookies are sent and treat the data obtained, we can distinguish:

    • Own cookies: those that are sent to the user's terminal equipment from a computer or domain managed by the editor itself and from which the service requested by the user is provided.
    • Third party cookies: those that are sent to the user's terminal equipment from a computer or domain that is not managed by the publisher, but by another entity that processes the data obtained through the cookies. When cookies are installed from a computer or domain managed by the publisher itself, but the information collected through them is managed by a third party, they cannot be considered as own cookies.

  2. Cookies according to the period of time they remain activated

    Depending on the length of time that they remain activated in the terminal equipment, we can distinguish:

    • Session cookies: type of cookies designed to collect and store data while the user accesses a web page. They are usually used to store information that only is kept to provide the service requested by the user on a single occasion (e.g. a list of products purchased).
    • Persistent cookies: type of cookies in which the data is still stored in the terminal and can be accessed and processed during a period defined by the person responsible for the cookie, which can range from a few minutes to several years.

  3. Cookies according to their purpose

    Depending on the purpose for which the data obtained through cookies are processed, we can distinguish between:

    • Technical cookies: those that allow the user to navigate through a web page, platform or application and the use of different options or services that exist in it, such as controlling traffic and data communication, identifying the session, access to restricted access parts, remember the elements that make up an order, perform the purchase process of an order, make a registration or participation in an event, use security elements during navigation, store content for the broadcast videos or sound or share content through social networks.
    • Personalization cookies: those that allow the user to access the service with some predefined general characteristics based on a series of criteria in the user's terminal, such as the language, the type of browser through which the user accesses the service, the regional configuration from where you access the service, etc.
    • Analytical cookies: those that allow the person responsible for them to monitor and analyse the behaviour of the users of the websites to which they are linked. The information collected through this type of cookies is used in the measurement of the activity of the websites, applications or platforms, and for the elaboration of navigation profiles of the users of said sites, applications and platforms, in order to introduce improvements in the analysis of the data of use made by the users of the service.

Cookies used on our website

The CBMSO website uses Google Analytics. Google Analytics is a simple and easy to use tool that helps website owners to measure how users interact with the content of the site. You can consult more information about the cookies used by Google Analitycs in this link.

Acceptance of the Cookies Policy

The CBMSO assumes that you accept the use of cookies if you continue browsing, considering that it is a conscious and positive action from which the user's consent is inferred. In this regard, you are previously informed that such behaviour will be interpreted that you accept the installation and use of cookies.

Knowing this information, it is possible to carry out the following actions:

  • Accept cookies: if the user presses the acceptance button, this warning will not be displayed again when accessing any page of the portal.
  • Review the cookies policy: the user can access to this page in which the use of cookies is detailed, as well as links to modify the browser settings.

How to modify the configuration of cookies

Using your browser you can restrict, block or delete cookies from any web page. In each browser the process is different, here we show you links on this particular of the most used browsers: