Currently, the lab is funded by two main grants listed below:
1. Synthetic Biology approaches for deciphering the logic of signal integration in complex bacterial promoters. FAPESP Young Investigators Awards - 12/22921-8. March 01, 2015 - February 28, 2019.
1. Synthetic Biology approaches for deciphering the logic of signal integration in complex bacterial promoters. FAPESP Young Investigators Awards - 12/22921-8. March 01, 2015 - February 28, 2019.
The ability to coordinate expression of thousands
of genes in response to different stimuli is an essential feature of any
live organism. However, current knowledge on this matter is largely
inferred from data on extant systems involving just a few regulatory
components. In this context, this project propose the adoption of a
genetically tractable experimental object (Escherichia coli) along with
the conceptual and material tools of Synthetic Biology for examining the
molecular mechanisms (hardware) and the underlying logic program
(software) that account for the regulatory behavior of complex
biological systems. The principal approach to this end will involve the
generation of synthetic promoter libraries assembled adjacent to
combinatorial arrays of upstream binding sequences for five known global
regulators (IHF, Fis, Crp, NarL and Fnr). The behavior of the resulting
promoter libraries will be thoroughly parameterized in single cells and
in populations as a whole for quantification of their transcriptional
capacity, kinetics and stochastic noise. The resulting data will be
employed to feed computational models for identifying general rules that
account for the regulation of the thereby generated promoters and
predict the outcome of new ones. We expect that the results of this
endeavor will contribute not only a fundamental understanding mechanisms
of signal integration in prokaryotic promoters, but will also produce
rules and methods for designing and building standardized, integrated
biological systems to accomplish many particular tasks of
biotechnological interest.
2. Deciphering the cis-regulatory elements related to the expression of cellulase-coding genes in Trichoderma reesei. MCTI/CNPq - 441833/2014-4. December 18, 2014 - November 18, 2017.
Cellulase producing microorganisms are of great interest for several biotechnological applications such as the production of bioethanol from plant biomass. In this sense, there is an increasing focus on the development of new technologies targeting the engineering of microorganisms to enhance the production of this enzyme class. This proposition aims the combination of different computational tools together with experimental setups in order to decipher the regulatory mechanisms related to the expression of cellulolytic enzymes in the filamentous fungus Trichoderma reesei. The project will focus on the identification of cis-regulatory elements in groups of co-regulated genes trigged by different growth conditions (such as in the presence of the cellulase-inducers cellulose or sophorose, or in the presence of the repressor glucose) identified using available RNA-seq data. The DNA motifs identified will be used to search databases for well-characterized cis-regulatory elements in order to allow the screening of new transcriptional factors potentially related to the control of cellulase expression in T. reesei. The new cis-regulatory elements will be characterized in vivo using transcriptional fusions of target promoters to the reporter gene GFP, while candidate transcriptional factors will be analyzed through the construction of mutant strains of T. reesei. In this way, the new regulatory information will be used to construct computational models aimed to simulate the response of the regulatory network to new environments, and the resulting predictions will be validated in vivo. The accomplishment of the proposition will potentially result in the generation of new knowledge on the regulatory mechanisms ruling cellulase expression in T. reesei, which will be crucial for future attempts to engineer this organism for application in the bioethanol industry.
3. High-throughput analysis of cis-regulatory logic in synthetic bacterial promoters.
Newton International Exchanges - The Royal Society - NI140137. March 10, 2015 - March 9, 2017.
Living cells can be programmed by incorporating integrated genetic circuits into their DNA. To date, circuits used to engineer conditional responses have been based on the combination of a limited number of genetic regulatory elements. Therefore, the aim of this project is to expand the toolbox of inputs that can be integrated into a synthetic circuit. In order to do that, we plan to design and engineer a library of single promoters that can act as individual logic gates by integrating new combinations of signals. The in silico design will be followed by an experimental validation 100 of these synthetic promoters using a specialized dual-reporter vector and a high-throughput robotic platform intended to measure gene expression at translational level
3. High-throughput analysis of cis-regulatory logic in synthetic bacterial promoters.
Newton International Exchanges - The Royal Society - NI140137. March 10, 2015 - March 9, 2017.
Living cells can be programmed by incorporating integrated genetic circuits into their DNA. To date, circuits used to engineer conditional responses have been based on the combination of a limited number of genetic regulatory elements. Therefore, the aim of this project is to expand the toolbox of inputs that can be integrated into a synthetic circuit. In order to do that, we plan to design and engineer a library of single promoters that can act as individual logic gates by integrating new combinations of signals. The in silico design will be followed by an experimental validation 100 of these synthetic promoters using a specialized dual-reporter vector and a high-throughput robotic platform intended to measure gene expression at translational level
