Inglés (Estados Unidos)

ibbtec@unican.es

Fernando de la Cruz Calahorra (IP)

fernando.cruz@unican.es
942 201942
Intergenomics
Principal Investigator
Microbiology & Genomics
Department of Microbiology & Genomics

The Intergenomics Group is composed of around 20 researchers with a common general research focus on plasmid biology and, more specifically, the mechanism of bacterial conjugation. Among the members of the group there are experts in microbiology, bacterial genetics, protein engineering, protein purification, crystallography, electron microscopy and biocatalysis. This makes the Intergenomics group a powerful team that can work independently or in cooperation with other research groups.

Intergenomics

Research lines

– Evolution and Ecology:
• Classification of conjugative and mobilizable plasmids based on their relaxase sequences.
• Conjugative systems of Cyanobacteria and Actinomycetes.
– Molecular Engines: Protein and DNA transporters across bacterial membranes
– Protein Engineering: Conjugative relaxases as a target for the inhibition of the dissemination of antibiotic resistance.
– Systems Biology

Funding

- Nuevas estrategias para el control de infecciones nosocomiales. INNOECO RTC-2015-3184-1.

“Promover el desarrollo tecnológico, la innovación y una investigación de calidad”

- Plásmidos ortogonales para Biología Sintética y de Sistemas. Ministerio de Educación (BFU2011-26608).
- Bacterial Computing with Engineered Populations (BACTOCOM). European Union 7th Framework. Programme, Area Information and Communication Technologies (FP7-ICT-2009-4; Proyecto nº 248919).
- EVOTAR: Evolution and transfer of antibiotic resistance (Project no. 282004). European Union FP7-HEALTH 2011.2.3.1-2.
- Diversidad y distribución de plásmidos de bacterias ácido-lácticas. Acción Integrada Hispano-Serbia. PRI-AIBSE-2011-1186. IP: Fernando de la Cruz
- INGENIERÍA GENÉTICA DE ESCHERICHIA COLI PARA MEJORAR LA PRODUCCIÓN DE LÍPIDOS RICOS EN ÁCIDOS GRASOS OMEGA-3 (TF16-XX-003), cofinanciado por SODERCAN S.A. y el Programa Operativo FEDER

Highlighting the potential of Synechococcus elongatus PCC 7942 as platform to produce α-linolenic acid through an updated genome-scale metabolic modeling

Santos-Merino M, Gargantilla-Becerra Á, de la Cruz F, Nogales J

Front Microbiol. 2023 Mar 14;14:1126030.

Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors

Fernandez-Lopez R, Ruiz R, Del Campo I, Gonzalez-Montes L, Boer DR, de la Cruz F, Moncalian G.

Nucleic Acids Res. 2022 Nov 11;50(20):11938-11947

Characterization of the DNA Binding Domain of StbA, A Key Protein of A New Type of DNA Segregation System

Quèbre V, Del Campo I, Cuevas A, Siguier P, Rech J, Le PTN, Ton-Hoang B, Cornet F, Bouet JY, Moncalian G, de la Cruz F, Guynet C.

J Mol Biol. 2022 Oct 15;434(19):167752.

Isolation and phenotypic and genomic characterization of Tetragenococcus spp. from two Spanish traditional blue-veined cheeses made of raw milk

Rodríguez J, González-Guerra A, Vázquez L, Fernández-López R, Flórez AB, de la Cruz F, Mayo B.

Int J Food Microbiol. 2022 Apr 8;371:109670.

Conjugation Inhibitors Effectively Prevent Plasmid Transmission in Natural Environments

Palencia-Gándara C, Getino M, Moyano G, Redondo S, Fernández-López R, González-Zorn B, de la Cruz F.

mBio. 2021 Aug 31;12(4):e0127721.

Integrated strategy for the separation of endotoxins from biofluids. LPS capture on newly synthesized protein

Basauri A., Fallanza M., Giner-Robles L., Fernandez-Lopez R., Moncalián G., de la Cruz F., Ortiz I.

Separation and Purification Technology. Volume 255, 15 January 2021, 117689

Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids

Santiago Redondo-Salvo, Raúl Fernández-López, Raúl Ruiz, Luis Vielva, María de Toro, Eduardo P C Rocha, M Pilar Garcillán-Barcia, Fernando de la Cruz

Nat Commun. 2020 Jul 17;11(1):3602. doi: 10.1038/s41467-020-17278-2.

Biochemical interactions between LPS and LPS-binding molecules

Basauri A, González-Fernández C, Fallanza M, Bringas E, Fernandez-Lopez R, Giner L, Moncalián G, de la Cruz F, Ortiz I.

Crit Rev Biotechnol. 2020 May;40(3):292-305. doi: 10.1080/07388551.2019.1709797. Epub 2020 Jan 13.

ArdC, a ssDNA-binding protein with a metalloprotease domain, overpasses the recipient hsdRMS restriction system broadening conjugation host range

Lorena González-Montes, Irene Del Campo, M Pilar Garcillán-Barcia, Fernando de la Cruz, Gabriel Moncalián

PLoS Genet. 2020 Apr 29;16(4):e1008750. doi: 10.1371/journal.pgen.1008750. eCollection 2020 Apr.

Conjugation inhibitors compete with palmitic acid for binding to the conjugative traffic ATPase TrwD, providing a mechanism to inhibit bacterial conjugation

García-Cazorla Y, Getino M, Sanabria-Ríos DJ, Carballeira NM, de la Cruz F, Arechaga I, Cabezón E

J Biol Chem. 2018 Oct 26;293(43):16923-16930.

fabH deletion increases DHA production in Escherichia coli expressing Pfa genes.

Giner-Robles, L.; Lázaro, B.; de la Cruz, F. and Moncalián, G.

Heterologous Expression of a Thermophilic Diacylglycerol Acyltransferase Triggers Triglyceride Accumulation in Escherichia coli.

Lázaro, B.; Villa, J.A.; Santín, O.; Cabezas, M.; Milagre, C.D.F.; de la Cruz, F. and Moncalián, G.

Plos One. 12(4):e0176520. doi: 10.1371/journal.pone.0176520.

Conjugation Inhibitors and Their Potential Use to Prevent Dissemination of Antibiotic Resistance Genes in Bacteria

Cabezón E, de la Cruz F, Arechaga I.

Front Microbiol. 2017 Nov 30;8:2329. doi: 10.3389/fmicb.2017.02329. eCollection 2017.

Nutrient starvation leading to triglyceride accumulation activates the Entner Doudoroff pathway in Rhodococcus jostii RHA1.

Juárez A, Villa JA, Lanza VF, Lázaro B, de la Cruz F, Álvarez HM and Moncalián G.

Microbial Cell Factories 16,35. doi: 10.1186/s12934-017-0651-7.

Relaxosomes and plasmid transfer in Gram-negative bacteria.

Zechner, E.L.; Moncalián, G. and de la Cruz, F.

Current Topics in Microbiology and Immunology. 413:93-113. doi: 10.1007/978-3-319-75241-9_4.

Substrate translocation involves specific lysine residues of the central channel of the conjugative coupling protein TrwB.

Larrea D, de Paz HD, Matilla I, Guzmán-Herrador DL, Lasso G, de la Cruz F, Cabezón E, Llosa M. ol Genet Genomics. 2017 Jun 8. doi: 10.1007/s00438-017-1331-3. (Epub ahead of print)


“Promover el desarrollo tecnológico, la innovación y una investigación de calidad”

Fernando de la Cruz Calahorra (IP)

Intergenomics

Research lines

Funding

Highlighting the potential of Synechococcus elongatus PCC 7942 as platform to produce α-linolenic acid through an updated genome-scale metabolic modeling

Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors

Characterization of the DNA Binding Domain of StbA, A Key Protein of A New Type of DNA Segregation System

Isolation and phenotypic and genomic characterization of Tetragenococcus spp. from two Spanish traditional blue-veined cheeses made of raw milk

Conjugation Inhibitors Effectively Prevent Plasmid Transmission in Natural Environments

Integrated strategy for the separation of endotoxins from biofluids. LPS capture on newly synthesized protein

Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids

Biochemical interactions between LPS and LPS-binding molecules

ArdC, a ssDNA-binding protein with a metalloprotease domain, overpasses the recipient hsdRMS restriction system broadening conjugation host range

Conjugation inhibitors compete with palmitic acid for binding to the conjugative traffic ATPase TrwD, providing a mechanism to inhibit bacterial conjugation

fabH deletion increases DHA production in Escherichia coli expressing Pfa genes.

Heterologous Expression of a Thermophilic Diacylglycerol Acyltransferase Triggers Triglyceride Accumulation in Escherichia coli.

Conjugation Inhibitors and Their Potential Use to Prevent Dissemination of Antibiotic Resistance Genes in Bacteria

Nutrient starvation leading to triglyceride accumulation activates the Entner Doudoroff pathway in Rhodococcus jostii RHA1.

Relaxosomes and plasmid transfer in Gram-negative bacteria.

Substrate translocation involves specific lysine residues of the central channel of the conjugative coupling protein TrwB.

Design of Novel Relaxase Substrates Based on Rolling Circle Replicases for Bioconjugation to DNA Nanostructures.

Orthogonal protein assembly on DNA nanostructures using relaxases.

Comparative genomics of the conjugation region of F-like plasmids: five shades of F.

Concerted action of NIC relaxase and auxiliary protein MobC in RA3 plasmid conjugation.

Concerted action of NIC relaxase and auxiliary protein MobC in RA3 plasmid conjugation.

Genomics of high molecular weight plasmids isolated from an on-farm biopurification system.

Type IV traffic ATPase TrwD as molecular target to inhibit bacterial conjugation.

Type IV traffic ATPase TrwD as molecular target to inhibit bacterial conjugation.

Transcription factor-based biosensors enlightened by the analyte.

Rebooting the genome: The role of negative feedback in horizontal gene transfer.

Degenerate primer MOB typing of multiresistant clinical isolates of E. coli uncovers new plasmid backbones.

Towards an integrated model of bacterial conjugation.

Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages.

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences.

Molecular epidemiology and virulence of Escherichia coli O16:H5-ST131: comparison with H30 and H30-Rx subclones of O25b:H4-ST131.

A high security double lock and key mechanism in HUH relaxases controls oriT-processing for plasmid conjugation.

PipX, the coactivator of NtcA, is a global regulator in cyanobacteria.

Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion.

Plasmid conjugation from proteobacteria as evidence for the origin of xenologous genes in cyanobacteria.

Negative feedback and transcriptional overshooting in a regulatory network for horizontal gene transfer.

Use of limited proteolysis and mutagenesis to identify folding domains and sequence motifs critical for wax ester synthase/acyl coenzyme A:diacylglycerol acyltransferase activity.

Use of limited proteolysis and mutagenesis to identify folding domains and sequence motifs critical for wax ester synthase/acyl coenzyme A:diacylglycerol acyltransferase activity.

Genomic analysis of the emergence and evolution of multidrug resistance during a Klebsiella pneumoniae outbreak including carbapenem and colistin resistance.

Four main virotypes among extended-spectrum-β-lactamase-producing isolates of Escherichia coli O25b:H4-B2-ST131: bacterial, epidemiological, and clinical characteristics.

The transmembrane domain of the T4SS coupling protein TrwB and its role in protein-protein interactions.

Subcellular location of the coupling protein TrwB and the role of its transmembrane domain.

Functional interactions of VirB11 traffic ATPases with VirB4 and VirD4 molecular motors in type IV secretion systems.

Breaking and joining single-stranded DNA: the HUH endonuclease superfamily.

Catalytic domain of plasmid pAD1 relaxase TraX defines a group of relaxases related to restriction endonucleases.

Structural independence of conjugative coupling protein TrwB from its Type IV secretion machinery

Multicellular computing using conjugation for wiring.

CRISPR-Cas systems preferentially target the leading regions of MOBF conjugative plasmids.

Evolution of Conjugation and Type IV Secretion Systems.

Ordering the bestiary of genetic elements transmissible by conjugation.

The hexameric structure of a conjugative VirB4 protein ATPase provides new insights for a functional and phylogenetic relationship with DNA translocases.

A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings.

Determination of conjugation rates on solid surfaces.

Interaction between relaxase MbeA and accessory protein MbeC of the conjugally mobilizable plasmid ColE1.

Regulation of the type IV secretion ATPase TrwD by magnesium: implications for the catalytic mechanism of the secretion ATPase superfamily.

Autoinhibitory regulation of TrwK, an essential VirB4 ATPase in type IV secretion systems.

The conjugative DNA translocase TrwB is a structure specific DNA-binding protein.

Relaxase DNA binding and cleavage are two distinguishable steps in conjugative DNA processing that involve different sequence elements of the nic site.

Miguel Baez Martín

Marina Domínguez Quintero

Raúl Fernández López

Sheila González Gutiérrez

Raquel Gutiérrez Lanza

Alfonso Mendaña Gomez

Irene Sanz Puente

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