Research interests and Projects

1. Research interests

The Prokaryotic Development Group (BIO318), that has the honor of holding the “University of Granada for Excellent Research Award", performs research with the multicellular bacterium Myxococcus xanthus. Our main interest is to discover the molecular mechanisms involved in the M. xanthus multifaceted social behaviors that maximize the use of resources and their survival by adopting a multicellular lifestyle, in a way that resembles to eukaryotic organisms. We also perform research about the global molecular response of bacteria to the different changes that they face in the environment, such as the presence of copper and other metals. We are also interested in deciphering the extraordinary predatory capacity of M. xanthus. This bacterium secretes a plethora of secondary metabolites to kill the prey, but many of them remains silence under laboratory conditions. Interactions between microorganisms may increase the production of these secondary metabolites and/or lead to the discovery of new metabolic compounds, so the co-culture predator-prey should be considered as a new biotechnological approach in the current antibiotic crisis era. For these reasons, the World Health Organization has proposed in a recent report “reorientating research to better understand the role of bacteria and their ecological relationships” as a guideline to effectively deal with antibiotic resistance to avoid drifting back to a pre-antibiotic era. We are using "omic" technologies to decipher the interaction of M. xanthus with other soil bacteria such as Streptomyces or Sinorhizobium meliloti to try to awake silenced genes. We are also studying the role of iron and siderophores in predation and the impact of predation of the symbiosis rhizobium-leguminous plants. The group combines classical microbiology, molecular biology and microscopy techniques, with massive sequencing, transcriptomic, bioinformatics, and comparative genomics technologies.

We have participate in more than 30 competitive research projects, including 11 National projects, 2 projects with companies, 1 FEDER project, 1 Project for Excellence Research from Junta de Andalucía, 1 CONSOLIDER-INGENIO, 1 COST ACTION, 1 Granada Research of Excellence Iniciative on Biohealth (GREIB), several Interchange project and several Integrated Actions.

We have organized the 1ª Reunión Científica de la Red Nacional de Genómica Bacteriana, the 34^th International Conference on the Biology of Myxobacteria and two International Workshops.

The formation capacity of the group is extensive. We have supervised 8 doctoral thesis, more than 25 master thesis and more than 35 experimental final degree projects.

The group has published in prestigious scientific journals such as Nature of Biotechnology, Cell, Proceedings of the National Academy of Science, Nucleic Acids Research, Annual Review in Microbiology, Computational and Structural Biotechnology Journal, PLos Genetics, Environmental Microbiology, Journal of Biological Chemistry, Molecular Microbiology, etc

Myxobacteria: models of prokaryotics multicellularity and bacterial predation

Myxobacteria are δ-proteobacteria that exhibit a peculiar multicellular cell cycle:

(A) In presence of nutrients cells move in a coordinate manner, forming swarms. When swarms contact with the prey, cells penetrates the prey colony and lyse the cells. (B) In starvation, cells moving collectively, start a developmental program and interchange extracellular chemical signals as well as physical contact signals to first form aggregates and later build millimeter-size upright fruiting bodies filled with differentiated , reproductive and environmental resistant cells named as myxospores (rounds cells), surrounded by other two subpopulations showing division of labor: a monolayer of aligned non-reproductive peripheral rods (yellow cells) and cells that undergo altruistic obligatory autolysis by programmed cell death (transparent cells). Myxospores ensure the surviving during starvation or desiccation and are able to disperse to other environments and germinate when nutrient conditions ameliorate. (Muñoz-Dorado et al., 2016)

The complex Signal transduction in myxobacteria

Completion of the multicellular process requires a controlled cell-cell interaction. M. xanthus posseses three main types of signal transduction systems: two component systems, extracytoplasmic function sigma factors (ECF) and Serine/Threonine protein kinases (STPK). Our group is interested in the study of signal transduction mechanisms during development by using functional classic molecular biology, genomic and transcriptomic approaches.

Deciphering of Myxococcus xanthus copper global response

M. xanthus is a soil bacterium and therefore it has to complete the life cycle in presence of the soil natural compounds. One of these compounds is copper, which is present in soils to concentrations that fluctuate between 2-100 mg/Kg. This metal is essential for life because it is used as cofactor by many enzymes involved in vital processes. However, copper is also extremely toxic mainly through the formation of reactive oxygen species. Due to this dual effect, cells have different mechanisms to ensure appropriate intracellular copper levels. M. xanthus give us the opportunity to study cell global response during a complete life cycle. This research, that is being performed using classic molecular biology and functional genomic techniques, has allowed to described a new group of metal dependent ECF sigma factors.

Copper induces carotenoids in M. xanthus

(Moraleda-Muñoz et al., 2005)

M. xanthus global copper response (Pérez et al., 2018)

Mechanism of action of a new group of CorE-like metal dependent ECF sigma factors (Pérez et al., 2018)

The largest known bacterial genomes

Several myxobacterial strains sequenced possess genomes among the largest ones described in prokaryotes, making them excellent models for the study of genome expansion. The expansion of myxobacterial genomes are mainly due to gene duplication and divergence. Our group is studying the evolution of several families of paralogs.

Expansion of Serine/Threonine protein kinases in the myxobacteria genomes (Pérez et al., 2008)

Bacterial predation: basic studies and ecological, evolutoinary, biotechnological and agricultural consequences

Bacterial predation has been proposed as an evolutionary driving force. The structure and diversity of predatory bacterial community is beginning to be recognize as an important factor in biodiversity due to its potential role in controlling and modelling bacterial populations in the enviroment. M. xanthus is a soil bacteria that is able to prey upon a variety of other bacteria as well as fungi. We are studying the strategies of M. xanthus predation on other important soil bacteria such as Streptomyces or Shinorhizobium. The predatosome (M. xanthus genes involved in predation) and defensome (S. meliloti genes involved in the defense of the prey) are being studied by using massive sequecing (RNA seq), genomic and classical molecular biology and microbiology techiques. The basic research will shed light from a basic point of view to the unknown killing processes used by these small predators. The fact that these bacteria have the genetic potential to produce a large battery of antibiotics, the in vivo study against prey, will help us to discover new products with biological activity and may open new horizons in their application in biocontrol processes against pathogenic bacteria, as an alternative to antibiotics. On the other hand, the defense mechanisms of the prey will help us to unveil new strategies of bacteria against antibiotics.

M. xanthus versus S. versicolor (Pérez et al., 2016)

M. xanthus versus different strains of S. meliloti (Muñoz-Dorado et al., 2016)

Defense mechanisms in the prey with biotechnological applications (Pérez et al., 2020)

A. Silenced antibiotics are induced in the prey during the predatory process. In the pictures, M xanthus (Mx, predator) induces in Streptomyces coelicolor (Sc, prey) the blue antibiotic actinorhodin, in solid and liquid media. B. Novel antibiotic resistance mechanisms have been discovered in B. thuringensis: myxovirescin TA glucosylation. C. Other physical/chemical defenses mechanisms induced by M. xanthus predation in different bacteria. Galactoglucan (left picture) and melanin (middle picture) protect Sinorhizobium meliloti from predation. M. xanthus induces development in Streptomyces (right picture). Pictures from panel A and right picture from panel C are reproduced from Pérez et al. (2011) Microb Biotechnol 4: 175–183. Left picture in panel C is adapted from Muñoz-Dorado et al., (2016) Front Microbiol 7: 781. Middle picture in panel C is from Contreras-Moreno et al. (2020) Front Microbiol 11: 94.

2. Research Projects

2.1. Research Funded Projects

· Unravelling the potential of LysM-domain proteins to awaken silent secondary metabolites genes in predatory bacteria through predator-prey interactions. LYSM. HORIZON.1.2 - Marie Skłodowska-Curie Actions (MSCA).  https://cordis.europa.eu/project/id/101106411. Grant agreement ID: 101106411. Investigador principal: Francisco Javier Marcos Torres.

· Bacterias depredadoras: nuevas estrategias en la crisis de los antibióticos. 2021-2023. Proyectos Frontera. FEDER. ANDALUCIA. A‐BIO‐126‐UGR20. Investigadores principales: Juana Pérez Torres y Aurelio Moraleda Muñoz.

· Estudios sobre depredación bacteriana y su impacto en agricultura. 2021-2024. MCI. Proyectos de I+D+i en el marco de los programas estatales de generación de conocimiento y fortalecimiento científico y tecnológico del sistema de I+D+i. PID2020-112634GB-I00. Investigadores principales: Aurelio Moraleda Muñoz y José Muñoz Dorado.

· Depredación bacteriana: estudio del predatosoma de Myxococcus xanthus y el defensoma de Sinorhizobium meliloti. 2016-2020. MEC. BFU2016-75425-P (Programa estatal de fomento de la investigación científica y técnica de excelencia, Subprograma estatal de generación de conocimiento). Investigadores principales: Aurelio Moraleda Muñoz y José Muñoz Dorado.

· Red de Excelencia. Microgen-NET. 2017-2018. Ministerio de Economía y Competitividad: Acciones de Dinamización. Ref. Consolider CGL2015-71523-REDC. Coordinador: Francisco Rodríguez Valera, Investigador responsable de la Universidad de Granada: José Muñoz Dorado.

· Estudios sobre rutas de transduccion de señales mediadas por proteínas quinasas de tipo eucariota durante el desarrollo. 2013-2015. MEC. Ref. BFU2012-33248. Investigador principal: José Muñoz Dorado.

· MICROBIAL COMPARATIVE GENOMICS. 2009-2014. MCyT: CONSOLIDER-INGENIO 2010. Ref. CSD2009-00006 Coordinador: Francisco Rodríguez Valera, Investigador responsable de la Universidad de Granada: José Muñoz Dorado.

· Las quinasas de Myxococcus xanthus como modelo de evolución de parálogos. 2010- 2012. MCyT. Ref. BFU2009-07565 (Subprograma BMC)." Investigador principal: José Muñoz Dorado.

· Respuesta global al cobre en Myxococcus xanthus. 2007-2010. Proyecto Excelencia Junta de Andalucía. Ref. CVI1377. Investigador principal: José Muñoz Dorado.

· Acción integrada entre la Universidad de Granada y Universidad de Georgia. 2009-2010. PLAN PROPIO UNIVERSIDAD GRANADA. Investigador principal: José Muñoz Dorado.

· Oxidasas multicobre de Myxococcus xanthus: regulación y función durante el crecimiento vegetativo y el ciclo de desarrollo. 2006-2009. MEC. Ref. BFU2006-00972/BMC. Investigador principal: José Muñoz Dorado.

· Expression, purification and structural characterization of a multicopper oxidase of Myxococcus xanthus. 2006-2007. MEC. Acción integrada Hispano Portuguesa. MEC. Ref: HP2005-0034. Coordinadores: José Muñoz Dorado y Ligia O. Martins.

· RED NACIONAL DE GENÓMICA BACTERIANA. 2004-2007. Genoma España y MEC. Coordinadores: Fernando Rojo (Centro Nacional de Biotecnología, Madrid) y Alex Mira Obrador (Universidad Miguel Hernández).

· Estudios sobre las rutas de transducción de señales en las que intervienen proteínas quinasas y fosfatasas de tipo eucariótico en Myxococcus xanthus. 2003-2006. MCYT. Ref: BMC2003-02038. Investigador principal: José Muñoz Dorado.

· Búsqueda de los elementos corriente arriba y abajo de los sistemas reguladores de dos componentes PhoR1-PhoP1, PhoR2-PhoP2 y PhoR3-PhoP3 de Myxococcus xanthus. 2000-2003. Dirección General de Enseñanza Superior e Investigación Técnica. Ref: BMC2002-03012. Investigador principal: José Muñoz Dorado.

· RED TEMÁTICA del programa de Biotecnología: "Biodegradacion de lignina y hemicelulosa. Aspectos enzimáticos, químicos y moleculares, y sus aplicaciones industriales y medioambientales". MCyT.Refs: BIO95-1057-E, CICYT-BIO98-1841-E; CICYT2002, BIO2004-20903-E, Bio2009-07866-E, BIO2011-15394-E. 1993-2014.Coordinador: Susana Camarero Fernández (Centro de Investigaciones Biológicas, Madrid, CSIC).

2.2. Research Competitives Grants

· Predoctoral contract. FEDER. Andalucia. Francisco Javier Contreras Moreno (15/06/2022- 15/06/2023). Investigador responsable: Juana Pérez Torres

· Predoctoral contract. Junta de Andalucía. Programa de empleo juvenil. Fondo Social Europeo. Subprograma Joven investigador. Lucía Cabello Alemán (06/14/2021-21/05/2021). Investigador responsable: Aurelio Moraleda Muñoz.

· Predoctoral contract. Junta de Andalucía. Programa de empleo juvenil. Fondo Social Europeo. Subprograma Joven investigador. Ana Alberola Romano (06/04/2021-21/05/2021). Investigador responsable: Aurelio Moraleda Muñoz.

· Predoctoral contract University of Granada from the research project BFU2016-75425-P. 31/07/2019 -29/12/2019. Francisco Javier Contreras Moreno. Investigador responsable: Aurelio Moraleda Muñoz.

· Predoctoral contract. Junta de Andalucía. Programa de empleo juvenil. Fondo Social Europeo. Subprograma Joven investigador. 31/01/2018- 30/07/2019. Francisco Javier Contreras Moreno. Investigador responsable: Aurelio Moraleda Muñoz.

· Senior mobility grant Salvador de Madariaga. Ministerio de Educación. Juana Pérez Torres. 01/03/2018-30/06/2018.

· Senior mobility grant Salvador de Madariaga. Ministerio de Educación. José Muñoz Dorado. 01/03/2018-30/06/2018.

· Predoctoral contract. Junta de Andalucía. Programa de empleo juvenil. Fondo Social Europeo. Subprograma Contratos de personal técnico. 31/10/2017- 03/06/2018. María del Carmen Rodríguez López. Investigador responsable: Aurelio Moraleda Muñoz.

· Predoctoral contract. Junta de Andalucía. Programa de empleo juvenil. Fondo Social Europeo. Subprograma Contratos de personal técnico. 01/06/2017-26/10/2018. Natalia Isabel Garcia Tomsing. Investigador responsable: Aurelio Moraleda Muñoz.