General Description
The main goal of the group is to understand the molecular mechanisms related to gene regulation in prokaryotic and eukaryotic microorganisms through Systems and Synthetic Biology approaches.
Research Overview
Through the understanding of gene regulation mechanisms, the group aims to set new concepts and construct tools to engineer synthetic regulatory circuits in living cells for several biotechnological applications. For this, we combine molecular biology tools with computational biology approaches to unveil hidden aspect of gene regulation, through the construction and characterization of mutant strains, assaying promoters fused to GFP reporter, performing bioinformatic analysis of genomes and transcriptomes, and even elaborating mathematical models to simulate the process under investigation. Due to the high complexity and multidisciplinarity of the research performed in the lab, students from different areas of knowledge (such as biology, chemistry, physics, informatics, etc.) are welcome to join the lab. Furthermore, the main research interests of the lab are:
1. Development of new genetic tools for microorganisms
Aims the development of new techniques and tools to allow genetic manipulation of living organisms, focusing mainly on the construction of modular vectors optimised for gram-negative bacteria and filamentous fungi.
Silva-Rocha R, de Lorenzo V. Chromosomal integration of transcriptional fusions. Methods Mol Biol. 2014;1149:479-89.
Benedetti IM, de Lorenzo V, Silva-Rocha R. Quantitative, non-disruptive monitoring of transcription in single cells with a broad-host range GFP-luxCDABE dual reporter system. PLoS One. 2012;7(12):e52000.
Silva-Rocha R, Martínez-García E, Calles B, Chavarría M, Arce-Rodríguez A, de Las Heras A, Páez-Espino AD, Durante-Rodríguez G, Kim J, Nikel PI, Platero R, de Lorenzo V. The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res. 2013 Jan;41(Database issue):D666-75.
Silva-Rocha R, de Lorenzo V. A GFP-lacZ bicistronic reporter system for promoter analysis in environmental gram-negative bacteria. PLoS One. 2012;7(4):e34675.
2. Systems Biology
Aims to study the properties of gene regulatory networks of the organism of interest using bioinformatics and computational biology approaches to integrate high-throughput data of structural and functional genomics and transcriptomics.
Silva-Rocha R, Castro Ldos S, Antoniêto AC, Guazzaroni ME, Persinoti GF, Silva RN. Deciphering the cis-regulatory elements for XYR1 and CRE1 regulators in Trichoderma reesei. PLoS One. 2014 Jun 18;9(6):e99366.
Antoniêto AC, dos Santos Castro L, Silva-Rocha R, Persinoti GF, Silva RN. Defining the genome-wide role of CRE1 during carbon catabolite repression in Trichoderma reesei using RNA-Seq analysis. Fungal Genet Biol. 2014 Dec;73:93-103.
Kim J, Oliveros JC, Nikel PI, de Lorenzo V, Silva-Rocha R. Transcriptomic fingerprinting of Pseudomonas putida under alternative physiological regimes. Environ Microbiol Rep. 2013 Dec;5(6):883-91.
Silva-Rocha R, de Lorenzo V. The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space. Environ Microbiol. 2013 Jan;15(1):271-86.
Silva-Rocha R, de Lorenzo V. Noise and robustness in prokaryotic regulatory networks. Annu Rev Microbiol. 2010;64:257-75.
The main goal of the group is to understand the molecular mechanisms related to gene regulation in prokaryotic and eukaryotic microorganisms through Systems and Synthetic Biology approaches.
Research Overview
Through the understanding of gene regulation mechanisms, the group aims to set new concepts and construct tools to engineer synthetic regulatory circuits in living cells for several biotechnological applications. For this, we combine molecular biology tools with computational biology approaches to unveil hidden aspect of gene regulation, through the construction and characterization of mutant strains, assaying promoters fused to GFP reporter, performing bioinformatic analysis of genomes and transcriptomes, and even elaborating mathematical models to simulate the process under investigation. Due to the high complexity and multidisciplinarity of the research performed in the lab, students from different areas of knowledge (such as biology, chemistry, physics, informatics, etc.) are welcome to join the lab. Furthermore, the main research interests of the lab are:
1. Development of new genetic tools for microorganisms
Silva-Rocha R, de Lorenzo V. Chromosomal integration of transcriptional fusions. Methods Mol Biol. 2014;1149:479-89.
Benedetti IM, de Lorenzo V, Silva-Rocha R. Quantitative, non-disruptive monitoring of transcription in single cells with a broad-host range GFP-luxCDABE dual reporter system. PLoS One. 2012;7(12):e52000.
Silva-Rocha R, Martínez-García E, Calles B, Chavarría M, Arce-Rodríguez A, de Las Heras A, Páez-Espino AD, Durante-Rodríguez G, Kim J, Nikel PI, Platero R, de Lorenzo V. The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res. 2013 Jan;41(Database issue):D666-75.
Silva-Rocha R, de Lorenzo V. A GFP-lacZ bicistronic reporter system for promoter analysis in environmental gram-negative bacteria. PLoS One. 2012;7(4):e34675.
2. Systems Biology
Silva-Rocha R, Castro Ldos S, Antoniêto AC, Guazzaroni ME, Persinoti GF, Silva RN. Deciphering the cis-regulatory elements for XYR1 and CRE1 regulators in Trichoderma reesei. PLoS One. 2014 Jun 18;9(6):e99366.
Antoniêto AC, dos Santos Castro L, Silva-Rocha R, Persinoti GF, Silva RN. Defining the genome-wide role of CRE1 during carbon catabolite repression in Trichoderma reesei using RNA-Seq analysis. Fungal Genet Biol. 2014 Dec;73:93-103.
Kim J, Oliveros JC, Nikel PI, de Lorenzo V, Silva-Rocha R. Transcriptomic fingerprinting of Pseudomonas putida under alternative physiological regimes. Environ Microbiol Rep. 2013 Dec;5(6):883-91.
Silva-Rocha R, de Lorenzo V. The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space. Environ Microbiol. 2013 Jan;15(1):271-86.
Silva-Rocha R, de Lorenzo V. Noise and robustness in prokaryotic regulatory networks. Annu Rev Microbiol. 2010;64:257-75.
Guazzaroni ME, Silva-Rocha R, Ward RJ. Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening. Microb Biotechnol. 2015 Jan;8(1):52-64.
Guazzaroni ME, Silva-Rocha R. Expanding the logic of bacterial promoters using engineered overlapping operators for global regulators. ACS Synth Biol. 2014 Sep 19;3(9):666-75.
Silva-Rocha R, de Lorenzo V. Engineering multicellular logic in bacteria with metabolic wires. ACS Synth Biol. 2014 Apr 18;3(4):204-9.
Silva-Rocha R, de Lorenzo V. Broadening the signal specificity of prokaryotic promoters by modifying cis-regulatory elements associated with a single transcription factor. Mol Biosyst. 2012 Jul 6;8(7):1950-7.
Silva-Rocha R, de Lorenzo V. Implementing an OR-NOT (ORN) logic gate with components of the SOS regulatory network of Escherichia coli. Mol Biosyst. 2011 Aug;7(8):2389-96.
