Welcome to the Krell laboratory.

The Krell laboratory is part of the research group “Environmental Microbiology and Biodegradation”. The laboratory is located at the Estación Experimental del Zaidín in Granada (Spain) which is part of the Spanish National Research Council (CSIC).

 

Bioinformatic analysis of chemoreceptors with a C-terminal pentapeptide for CheR and CheB binding

Ortega, A., Krell, T. (2020) Comput. Struct. Biotechnol. J. 18:1947-1955.

We have analysed the totality of currently available chemoreceptor sequences and have investigated the presence of C-terminal pentapeptides. The main conclusions are:

  1. Approximately 10 % of bacterial chemoreceptors contain such pentapeptides.
  2. Almost no pentapeptide containing chemoreceptors are found in archaea.
  3. Pentapeptide containing chemoreceptors are more abundant in GRAM – than GRAM + bacteria
  4. Pentapeptides are present in cytosolic (7.5 %) as well as transmembrane (11.5 %) chemoreceptors.
  5. The abundance of chemoreceptors with C-terminal pentapeptides correlates negatively with the number of chemoreceptors per genome.
  6. The maximal number of pentapeptide containing receptors per genome is of 27.
  7. The abundance of pentapeptides differs largely in receptors with different ligand binding domains (LBD, figure below): almost 50 % of TarH domain containing chemoreceptors possess pentapeptides, whereas the families of GAF and PilJ domain containing receptors have almost no pentapeptides.
  8. Pentapeptides are always fused to the C-terminus of an MCP, regardless whether the last domain is an LBD or signaling domain.
  9. Bacteria that inhabit the human intestinal flora possess a high abundance of pentapeptide containing chemoreceptors.
  10. Pentapeptide containing chemoreceptors are found in 11 different phyla.
  11. Chemoreceptors with pentapeptides are highly abundant in the order Enterobacterales (36 %).
  12. The abundance of pentapeptide containing chemoreceptors in several orders that contain primarily bacteria with a free-living lifestyle is reduced such as 1 % for Pseudomonadales.

The physiological relevance of pentapeptide containing chemoreceptors remains to be established.

Understanding how new chemoreceptors evolve

Gavira et al. (2020) mBio 11, pii: e03066-19

Many bacteria possess a large number of chemoreceptors that each respond to different signal molecules and frequently genomes contain paralogous receptors that have arisen by gene duplication. We have studied chemoreceptor evolution using the three paralogous receptors PctA, PctB and PctC of Pseudomonas aeruginosa as examples. Whereas PctA is a broad range receptor that responds to most proteinogenic amino acids, PctB and PctC recognize preferentially L-Gln and GABA, respectively. In a stimulating collaboration with the laboratory of Igor Zhulin (Ohio State University) we show that pctA gene duplication in the common ancestor of the genus Pseudomonas led to pctC, whereas pctB originated through another, independent pctA duplication in the common ancestor of P. aeruginosa. The 3D structures of the ligand binding domains of these three receptors in complex with several ligands were solved in an excellent collaboration with the laboratory of Jose A. Gavira and reveal the structural basis for differential ligand recognition.

Identification of the molecular basis of nitrate chemotaxis

Martín-Mora et al. (2019) mBio 10(1); e02334-18

Nitrate is of central relevance in bacterial physiology and it is known for a long time that many bacteria are able to perform taxis towards nitrate. So far, data suggest that these movements are based on energy tactic mechanisms in which metabolic consequences of nitrate metabolism are monitored. In this article we report a mechanism for nitrate chemotaxis that is based on the specific recognition of this ligand by the periplasmatic PilJ-type sensor domain of the McpN chemoreceptor of Pseudomonas aeruginosa. Nitrate chemotaxis occurred only under nitrate limiting condition, an observation that is most likely due to the nitrate-mediated reduction of mcpN transcript levels. We report the 3D structure of the McpN sensor domain in complex with nitrate at a resolution of 1.3 Å in which one nitrate molecule was bound at the dimer interface. McpN homologues were identified in many bacteria and were particularly abundant in species that couple sulfur/sulfite oxidation with nitrate reduction. Nitrate chemotaxis is likely to be a widespread phenomenon with importance for the life cycle of ecologically diverse bacteria.

An auxin controls antibiotics production in bacteria

Matilla et al. (2018). Nucleic Acids Research

Antibiotics production is costly to the bacterial cell and therefore in many cases subject to strict regulation. However, there is limited knowledge on the environmental cues that control antibiotics production and their corresponding mechanisms. The transcriptional regulator AdmX of the plant-associated bacterium Serratia plymuthica A153 was shown to control the synthesis of the antibiotic andrimid. AdmX contains a ligand binding domain of which we speculated to bind environmental signals that modulate its activity. Using high throughput approaches and purified protein we screened some 1700 compounds for binding and identified the auxin indole-3-acetic acid (IAA) as ligand. Antibiosis assays showed that IAA reduces andrimid production in a dose-dependent manner leading to undetectable andrimid production at 400 µM. AdmX was shown to control the transcription of the genes encoding the biosynthetic andrimid cluster. IAA is produced by plants and bacteria, and our study shows that the synthesis of IAA by other plant-associated bacteria results in the inhibition of andrimid production, suggesting that IAA bacterial production corresponds to a mode of inter-species communication.

This work provides groundbreaking insight into environmental signals that control antibiotics production and has been published as Matilla et al. in Nucleic Acids Research.

 

 

Selected publications

Gavira JA, Gumerov VM, Rico-Jiménez M, Petukh M, Upadhyay AA, Ortega A, Matilla MA, Zhulin IB, Krell T. (2020) How Bacterial chemoreceptors evolve novel ligand specificities. mBio 11:e03066-19.

Ortega, A., Krell, T. (2020) Chemoreceptors with C-terminal pentapeptides for CheR and CheB binding are abundant in bacteria that maintain host interactions. Comput. Struct. Biotechnol. J. 18:1947-1955.

Martín-Mora, D., Ortega, A., Matilla, M.A., Martínez-Rodríguez, S., Gavira, J.A., Krell, T. (2019) The molecular mechanism of nitrate chemotaxis via direct ligand binding to the PilJ domain of McpN. mBio 10:e02334-18

Cerna-Vargas, J.P., Santamaría-Hernando, S., Matilla, M.A., Rodríguez-Herva, J.J., Daddaoua, A., Rodríguez-Palenzuela, P., Krell, T. López-Solanilla, E. (2019)  Chemoperception of specific amino acids controls phytopathogenicity in P. syringae pv. Tomato.  mBio 10:e01868-19.

Corral-Lugo A., Matilla M.A., Martín-Mora D., Silva Jiménez H., Mesa Torres N., Kato J., Hida A., Oku S., Conejero-Muriel M., Gavira J.A., Krell T. (2018). High-affinity chemotaxis to histamine mediated by the TlpQ chemoreceptor of the human pathogen Pseudomonas aeruginosa. mBio 9:e01894-18

Matilla M.A., Daddaoua A., Chini A., Morel B., Krell T. (2018). An auxin controls bacterial antibiotics production. Nucleic Acids Res. 46:11229-11238 46:11229-11238

Corral-Lugo A, Daddaoua A, Ortega A, Espinosa-Urgel M, Krell T. (2016) Rosmarinic acid is a homoserine lactone mimic produced by plants that activates a bacterial quorum-sensing regulatorScience Signaling 9(409):ra1.

García Fontana, C., Corral-Lugo, A., Krell, T. (2014) Specificity of the CheR2 Methyltransferase in Pseudomonas aeruginosa is Directed by C-Terminal Pentapeptides in ChemoreceptorsScience Signaling 7 (320) ra34.

Pineda-Molina, E., Reyes-Darias, J.A., Lacal, J., Ramos, J.L., García-Ruiz, J.M., Gavira, J.A., Krell, T. (2012) Evidence for chemoreceptors with bimodular ligand binding regions harboring two signal-binding sitesProc. Acad. Natl. Sci. USA. 109, 18926-18931.

Matilla, M.A., Krell, T. (2018) The effect of bacterial chemotaxis on host infection and pathogenicity. FEMS Microbiol Rev. 42:10.1093/femsre/fux052.

Ortega, Á., Zhulin, I.B., Krell, T. (2017) Sensory Repertoire of Bacterial Chemoreceptors. Microbiol. Mol. Biol. Rev. 81: e00033-17 .

Martín-Mora D, Reyes-Darias JA, Ortega A, Corral-Lugo A, Matilla MA, Krell T. (2016) McpQ is a specific citrate chemoreceptor that responds preferentially to citrate/metal ion complexes. Environ Microbiol.  18:3284-3295.

Fernández M, Morel B, Corral-Lugo A, Krell T. (2016) Identification of a chemoreceptor that specifically mediates chemotaxis toward metabolizable purine derivatives. Mol Microbiol. 99:34-42.

Reyes-Darias JA, García V, Rico-Jiménez M, Corral-Lugo A, Lesouhaitier O, Juárez-Hernández D, Yang Y, Bi S, Feuilloley M, Muñoz-Rojas J, Sourjik V, Krell T. (2015). Specific gamma-aminobutyrate (GABA) chemotaxis in Pseudomonads with different lifestyle. Mol. Microbiol. 97:488-501.

Garcia-Fontana C., Reyes-Darias J.A., Munoz-Martinez F., Alfonso C., Morel B., Ramos J.L., Krell T. (2013) High specificity in CheR methyltransferase function: CheR2 of Pseudomonas putida is essential for chemotaxis whereas CheR1 is involved in biofilm formation. J. Biol. Chem. 288 (26):18987-99.