{"id":20815,"date":"2026-04-13T11:02:20","date_gmt":"2026-04-13T10:02:20","guid":{"rendered":"https:\/\/cabd.es\/investigation\/departments\/cell-biology-and-biotechnology\/dra-francisca-reyes-ramirez\/"},"modified":"2026-11-03T11:35:49","modified_gmt":"2026-11-03T10:35:49","slug":"dra-francisca-reyes-ramirez","status":"publish","type":"page","link":"https:\/\/cabd.es\/en\/investigation\/departments\/multicelular-dynamics\/dra-francisca-reyes-ramirez\/","title":{"rendered":"Dra Francisca Reyes-Ram\u00edrez"},"content":{"rendered":"

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Multicellular Dynamics<\/p>\n

Regulatory mechanisms of gene expression in pollutant-degrading bacteria. Bioremediation<\/h1>\n

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Dra Francisca Reyes-Ram\u00edrez<\/h4>\n

Principal Investigator<\/p>\n

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Summary<\/h2>\n
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Many bacteria have the ability to degrade a variety of environmental pollutants and use them as growth substrates, making them a powerful tool for removing dangerous pollutants that are causing irreversible damage to the biosphere.<\/span><\/p>\n

Far from controlled conditions in the laboratory, microbial survival in natural habitats is often threatened by constantly fluctuating environmental conditions. Bacteria have learned to adapt to these stressful situations by adjusting their transcriptional profile and optimising gene expression. We study gene regulation and regulatory mechanisms (regulatory proteins, regulatory RNAs, induced gene function, etc.) that allow environmental pollutant-degrading bacteria to trigger the appropriate physiological and metabolic response to each environmental condition.<\/span><\/p>\n

We focus on two aspects of gene regulation and also in Bioremediation.<\/span><\/p>\n

<\/span><\/p>\n<\/div>\n

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  • The General Stress Response (GSR)<\/strong>\u00a0of\u00a0Sphingopyxis granuli<\/em>\u00a0TFA. TFA is\u00a0an Alphaproteobacterium capable of growing with the organic solvent tetralin (1,2,3,4-tetrahydronaphthalene) as its sole carbon and energy source. GSR is a global bacterial protective response against a wide variety of stresses. This response is controlled by two sigma factors of extracytoplasmic function (ECFG1-ECFG2). The regulatory cascade involves in addition to ECFs, the anti-sigma proteins NepR1-NepR2 and the anti-anti-sigma proteins PhyR1-PhyR2.<\/span><\/li>\n
  • The regulation of anaerobic metabolism<\/strong>\u00a0in\u00a0Sphingopyxis granuli<\/em>\u00a0TFA.\u00a0<\/strong>TFA is the only Sphingopyxis described with the ability to grow under anaerobic conditions by respiring nitrate. This new metabolism makes it particularly interesting as it allows it to inhabit new ecological niches. As part of this response, we are working on the identification and characterisation of small regulatory RNAs in anaerobiosis and the regulation of flagellar genes to oxygen availability.\u00a0<\/span><\/li>\n
  • Functional metagenomics for the identification of new enzymes and the development of biocatalysts of environmental interest.<\/strong>\u00a0The astonishing genetic diversity of the microbial world offers an extraordinary array of functions that have the potential to contribute to the development of industrial applications in many different fields. However, the vast majority of bacteria in natural ecosystems (more than 99%) cannot be cultured in the laboratory. This means that we are losing an enormous amount of information and its potential application using traditional techniques.\u00a0Functional metagenomics<\/strong>\u00a0allows access to all the genetic material of microorganisms in an environmental sample by direct extraction, without the need for prior cultivation of the microorganisms. Functional metagenomics involves extraction of DNA from a particular environment, creation of a metagenomic DNA library, expression of the library in the appropriate host and finally identification of an activity of interest in an enzymatic assay or growth on selective media. In this project we use metagenomic libraries to identify new enzymes in the area of\u00a0by-product revalorisation\u00a0<\/strong>(use of lignocellulosic waste for biofuel production and other biotechnological processes) and in the degradation of environmental pollutants such as\u00a0plastics<\/strong>.<\/span><\/li>\n<\/ul>\n
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        Five relevant publications<\/h2>\n
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        1. de Dios R.,\u00a0Santero E.,\u00a0Reyes-Ram\u00edrez F<\/strong>.\u00a0(2022). The functional differences between paralogous regulators define the control of the general stress response in\u00a0Sphingopyxis granuli<\/em>.\u00a0Environmental Microbiology<\/strong>,\u00a0doi.org\/10.1111\/1462-2920.15907<\/span><\/p>\n

        2. de Dios R.,\u00a0Santero E.,\u00a0Reyes-Ram\u00edrez F<\/strong>.\u00a0(2021). Extracytoplasmic Function \u03c3 Factors as Tools for Coordinating Stress Responses.\u00a0International Journal of Molecular Sciences. Special Issue Bacterial Proteins in Stress Management<\/strong>. 22 (Issue 8), 3900 doi.org\/10.3390\/ijms22083900<\/span><\/p>\n

        3. Gonz\u00e1lez-Flores, Y.E., de Dios, R.,\u00a0Reyes-Ram\u00edrez, F<\/strong>., Santero, E (2020). Identification of two fnr genes and characterisation of their role in the anaerobic switch in\u00a0Sphingopyxis granuli<\/em>\u00a0TFA.\u00a0Scientific Reports<\/strong>, 10: 21019; doi.org\/10.1038\/S41598-020-77927-w<\/span><\/p>\n

        4. de Dios, R., Rivas-Marin, E., Santero, E.,\u00a0Reyes-Ram\u00edrez F<\/strong>. (2020). Two paralogous EcfG \u03c3 factors hierarchically orchestrate the activation of the General Stress Response in\u00a0Sphingopyxis granuli<\/em>\u00a0TFA.\u00a0Scientific Reports<\/strong>, 10: 5177; doi.org\/10.1038\/s41598-020-62101-z<\/span><\/p>\n

        5. Floriano, B., Santero, E.,\u00a0Reyes-Ram\u00edrez F<\/strong>.\u00a0(2019): Biodegradation of Tetralin: Genomics, Gene Function and Regulation.\u00a0Genes<\/strong>\u00a0(10), 5: 339; doi.org\/10.3390\/genes10050339.<\/span><\/p>\n

        6. Gonz\u00e1lez-Flores, Y. de Dios R.,\u00a0Reyes-Ram\u00edrez F<\/strong>.\u00a0and Santero E. (2019). The response of\u00a0Sphingopyxis granuli<\/em>\u00a0strain TFA to the hostile anoxic\u00a0 condition.\u00a0Scientifics Reports<\/strong>\u00a09: 6297; doi.org\/10.1038\/s41598-019-42768-9.<\/span><\/p>\n

        7. Garcia-Romero, I., Perez-Pulido, A.J., Gonzalez-Flores, Y.E.,\u00a0Reyes-Ramirez, F<\/strong>., Santero, E. and B. Floriano. (2016). Genomic analysis of the nitrate-respiring\u00a0Sphingopyxis granuli<\/em>\u00a0(formerly Sphingomonas macrogoltabida) strain TFA.\u00a0BMC Genomics<\/strong>\u00a017:9; doi.10.1186\/s12864-016-2411-1<\/span><\/p>\n

        8. Ledesma-Garc\u00eda L., S\u00e1nchez-Azqueta A., Medina M.,\u00a0Reyes-Ram\u00edrez F<\/strong>., Santero E. (2016). Redox proteins of hydroxylating bacterial dioxygenases establish a regulatory cascade that prevents gratuitous induction of tetralin biodegradation genes.\u00a0Scientifics Reports<\/strong>\u00a06: 23848; doi: 10.1038\/srep23848<\/span><\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n

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        Lab members & Collaborators<\/h2>\n
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        Lab members<\/h3>\n

        Principal Investigator:<\/h4>\n

        Dr Francisca Reyes Ram\u00edrez, +34 954349053<\/p>\n

        Postdoctoral student:<\/h4>\n

        Inmaculada Garc\u00eda Romero<\/p>\n

        PhD student:<\/h4>\n

        Alberto Pires Costa<\/p>\n

        Master student<\/h4>\n

        Irene P\u00e1rraga Borrell
        Angela Rey Hidalgo<\/p>\n

        Collaborators<\/h3>\n

        Dr. Eva Mar\u00eda Camacho Fern\u00e1ndez (CABD, Universidad Pablo de Olavide, Sevilla)
        Dr. Fernado Govantes Romero (CABD, Universidad Pablo de Olavide, Sevilla)
        Dr. Antonio P\u00e9rez Pulido (CABD, Universidad Pablo de Olavide, Sevilla)
        Dr. Elena\u00a0 Rivas Mar\u00edn (CABD, Universidad Pablo de Olavide, Sevilla)
        Dr. Antonio Rosal Raya (\u00c1rea de Ingenier\u00eda Qu\u00edmica,\u00a0Universidad Pablo de Olavide, Sevilla)
        Dr. Hermann Heipieper (Center for Environmental Research, Leipzig, Germany)
        Dra. Milagros Medina (Facultad de Ciencias, Universidad de Zaragoza)
        Dr. Rub\u00e9n de Dios Barranco (Postdoc Ronan McCarthy, Uxbridge, London, United Kingdom)
        Dr. J\u00f6rg Vogel\u00a0 (Institute for Molecular Infection Biology at the University of W\u00fcrzburg, Germany)<\/p>\n

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        Multicellular Dynamics Regulatory mechanisms of gene expression in pollutant-degrading bacteria. Bioremediation Dra Francisca Reyes-Ram\u00edrez Principal Investigator Summary   Many bacteria have the ability to degrade a variety of environmental pollutants […]<\/p>\n","protected":false},"author":3024,"featured_media":0,"parent":20249,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"","footnotes":""},"class_list":["post-20815","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/pages\/20815","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/users\/3024"}],"replies":[{"embeddable":true,"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/comments?post=20815"}],"version-history":[{"count":14,"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/pages\/20815\/revisions"}],"predecessor-version":[{"id":27932,"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/pages\/20815\/revisions\/27932"}],"up":[{"embeddable":true,"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/pages\/20249"}],"wp:attachment":[{"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/media?parent=20815"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}