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Transcriptional regulation of central carbon metabolism in Pseudomonas aeruginosa.

Dolan SK, Pereira G, Silva-Rocha R, Welch M.

Microb Biotechnol. 2019 Jun 11. doi: 10.1111/1751-7915.13423. [Epub ahead of print]


Aspergillus fumigatus High Osmolarity Glycerol Mitogen Activated Protein Kinases SakA and MpkC Physically Interact During Osmotic and Cell Wall Stresses.

Manfiolli AO, Mattos EC, de Assis LJ, Silva LP, Ulaş M, Brown NA, Silva-Rocha R, Bayram Ö, Goldman GH.

Front Microbiol. 2019 May 7;10:918. doi: 10.3389/fmicb.2019.00918. eCollection 2019.


Expanding the Toolbox of Broad Host-Range Transcriptional Terminators for Proteobacteria through Metagenomics.

Amarelle V, Sanches-Medeiros A, Silva-Rocha R, Guazzaroni ME.

ACS Synth Biol. 2019 Apr 19;8(4):647-654. doi: 10.1021/acssynbio.8b00507. Epub 2019 Apr 9.


A phylogenetically conserved hnRNP type A/B protein from squid brain.

Lopes GS, Lico DTP, Silva-Rocha R, de Oliveira RR, Sebollela A, Paçó-Larson ML, Larson RE.

Neurosci Lett. 2019 Mar 23;696:219-224. doi: 10.1016/j.neulet.2019.01.002. Epub 2019 Jan 2.


Genomic and Postgenomic Approaches to Understand Environmental Microorganisms.

Guazzaroni ME, Platero RA, Silva-Rocha R.

Int J Genomics. 2018 Oct 24;2018:4915348. doi: 10.1155/2018/4915348. eCollection 2018. No abstract available.


Systems and Synthetic Biology Approaches to Engineer Fungi for Fine Chemical Production.

Martins-Santana L, Nora LC, Sanches-Medeiros A, Lovate GL, Cassiano MHA, Silva-Rocha R.

Front Bioeng Biotechnol. 2018 Oct 3;6:117. doi: 10.3389/fbioe.2018.00117. eCollection 2018. Review.


The Duality of the MAPK Signaling Pathway in the Control of Metabolic Processes and Cellulase Production in Trichoderma reesei.

de Paula RG, Antoniêto ACC, Carraro CB, Lopes DCB, Persinoti GF, Peres NTA, Martinez-Rossi NM, Silva-Rocha R, Silva RN.

Sci Rep. 2018 Oct 8;8(1):14931. doi: 10.1038/s41598-018-33383-1.


The art of vector engineering: towards the construction of next-generation genetic tools.

Nora LC, Westmann CA, Martins-Santana L, Alves LF, Monteiro LMO, Guazzaroni ME, Silva-Rocha R.

Microb Biotechnol. 2019 Jan;12(1):125-147. doi: 10.1111/1751-7915.13318. Epub 2018 Sep 26. Review.


Boosting Secondary Metabolite Production and Discovery through the Engineering of Novel Microbial Biosensors.

de Frias UA, Pereira GKB, Guazzaroni ME, Silva-Rocha R.

Biomed Res Int. 2018 Jul 9;2018:7021826. doi: 10.1155/2018/7021826. eCollection 2018. Review.


Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in Escherichia coli.

Westmann CA, Alves LF, Silva-Rocha R, Guazzaroni ME.

Front Microbiol. 2018 Jun 20;9:1344. doi: 10.3389/fmicb.2018.01344. eCollection 2018.


Calibrating Transcriptional Activity Using Constitutive Synthetic Promoters in Mutants for Global Regulators in Escherichia coli.

Sanches-Medeiros A, Monteiro LMO, Silva-Rocha R.

Int J Genomics. 2018 Mar 21;2018:9235605. doi: 10.1155/2018/9235605. eCollection 2018.


Engineering Complexity in Bacterial Regulatory Circuits for Biotechnological Applications.

Westmann CA, Guazzaroni ME, Silva-Rocha R.

mSystems. 2018 Apr 10;3(2). pii: e00151-17. doi: 10.1128/mSystems.00151-17. eCollection 2018 Mar-Apr.


Loving the poison: the methylcitrate cycle and bacterial pathogenesis.

Dolan SK, Wijaya A, Geddis SM, Spring DR, Silva-Rocha R, Welch M.

Microbiology. 2018 Mar;164(3):251-259. doi: 10.1099/mic.0.000604. Epub 2018 Jan 22.


Transcriptome-wide survey of gene expression changes and alternative splicing in Trichophyton rubrum in response to undecanoic acid.

Mendes NS, Bitencourt TA, Sanches PR, Silva-Rocha R, Martinez-Rossi NM, Rossi A.

Sci Rep. 2018 Feb 6;8(1):2520. doi: 10.1038/s41598-018-20738-x.


Galectin-3 impacts Cryptococcus neoformans infection through direct antifungal effects.

Almeida F, Wolf JM, da Silva TA, DeLeon-Rodriguez CM, Rezende CP, Pessoni AM, Fernandes FF, Silva-Rocha R, Martinez R, Rodrigues ML, Roque-Barreira MC, Casadevall A.

Nat Commun. 2017 Dec 6;8(1):1968. doi: 10.1038/s41467-017-02126-7.


Systematic identification of novel regulatory interactions controlling biofilm formation in the bacterium Escherichia coli.

Amores GR, de Las Heras A, Sanches-Medeiros A, Elfick A, Silva-Rocha R.

Sci Rep. 2017 Dec 1;7(1):16768. doi: 10.1038/s41598-017-17114-6.


Emergent Properties in Complex Synthetic Bacterial Promoters.

Monteiro LMO, Arruda LM, Silva-Rocha R.

ACS Synth Biol. 2018 Feb 16;7(2):602-612. doi: 10.1021/acssynbio.7b00344. Epub 2017 Nov 14.


Aspergillus fumigatus protein phosphatase PpzA is involved in iron assimilation, secondary metabolite production, and virulence.

Manfiolli AO, de Castro PA, Dos Reis TF, Dolan S, Doyle S, Jones G, Riaño Pachón DM, Ulaş M, Noble LM, Mattern DJ, Brakhage AA, Valiante V, Silva-Rocha R, Bayram O, Goldman GH.

Cell Microbiol. 2017 Dec;19(12). doi: 10.1111/cmi.12770. Epub 2017 Aug 17.


The Aspergillus fumigatus CrzA Transcription Factor Activates Chitin Synthase Gene Expression during the Caspofungin Paradoxical Effect.

Ries LNA, Rocha MC, de Castro PA, Silva-Rocha R, Silva RN, Freitas FZ, de Assis LJ, Bertolini MC, Malavazi I, Goldman GH.

MBio. 2017 Jun 13;8(3). pii: e00705-17. doi: 10.1128/mBio.00705-17.


Deletion of pH Regulator pac-3 Affects Cellulase and Xylanase Activity during Sugarcane Bagasse Degradation by Neurospora crassa.

Campos Antoniêto AC, Ramos Pedersoli W, Dos Santos Castro L, da Silva Santos R, Cruz AH, Nogueira KM, Silva-Rocha R, Rossi A, Silva RN.

PLoS One. 2017 Jan 20;12(1):e0169796. doi: 10.1371/journal.pone.0169796. eCollection 2017.


The Aspergillus fumigatus SchASCH9 kinase modulates SakAHOG1 MAP kinase activity and it is essential for virulence.

Alves de Castro P, Dos Reis TF, Dolan SK, Oliveira Manfiolli A, Brown NA, Jones GW, Doyle S, Riaño-Pachón DM, Squina FM, Caldana C, Singh A, Del Poeta M, Hagiwara D, Silva-Rocha R, Goldman GH.

Mol Microbiol. 2016 Nov;102(4):642-671. doi: 10.1111/mmi.13484. Epub 2016 Oct 7.


The Post-genomic Era of Trichoderma reesei: What's Next?

Gupta VK, Steindorff AS, de Paula RG, Silva-Rocha R, Mach-Aigner AR, Mach RL, Silva RN.

Trends Biotechnol. 2016 Dec;34(12):970-982. doi: 10.1016/j.tibtech.2016.06.003. Epub 2016 Jul 6. Review.


Pre-mRNA splicing is modulated by antifungal drugs in the filamentous fungus Neurospora crassa.

Mendes NS, Silva PM, Silva-Rocha R, Martinez-Rossi NM, Rossi A.

FEBS Open Bio. 2016 Mar 14;6(4):358-68. doi: 10.1002/2211-5463.12047. eCollection 2016 Apr.


Trichoderma reesei CRE1-mediated Carbon Catabolite Repression in Re-sponse to Sophorose Through RNA Sequencing Analysis.

Antoniêto AC, de Paula RG, Castro Ldos S, Silva-Rocha R, Persinoti GF, Silva RN.

Curr Genomics. 2016 Apr;17(2):119-31. doi: 10.2174/1389202917666151116212901.


Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories.

Amores GR, Guazzaroni ME, Arruda LM, Silva-Rocha R.

Curr Genomics. 2016 Apr;17(2):85-98. doi: 10.2174/1389202917666151116212255.


Understanding the Role of the Master Regulator XYR1 in Trichoderma reesei by Global Transcriptional Analysis.

Dos Santos Castro L, de Paula RG, Antoniêto AC, Persinoti GF, Silva-Rocha R, Silva RN.

Front Microbiol. 2016 Feb 16;7:175. doi: 10.3389/fmicb.2016.00175. eCollection 2016.


Transcription factor levels enable metabolic diversification of single cells of environmental bacteria.

Guantes R, Benedetti I, Silva-Rocha R, de Lorenzo V.

ISME J. 2016 May;10(5):1122-33. doi: 10.1038/ismej.2015.193. Epub 2015 Dec 4.


High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2.

Kim J, Pérez-Pantoja D, Silva-Rocha R, Oliveros JC, de Lorenzo V.

Environ Microbiol. 2016 Oct;18(10):3327-3341. doi: 10.1111/1462-2920.13054. Epub 2015 Oct 22.


Engineering Synthetic cis-Regulatory Elements for Simultaneous Recognition of Three Transcriptional Factors in Bacteria.

Amores GR, Guazzaroni ME, Silva-Rocha R.

ACS Synth Biol. 2015 Dec 18;4(12):1287-94. doi: 10.1021/acssynbio.5b00098. Epub 2015 Aug 31.


The impact of chromatin remodelling on cellulase expression in Trichoderma reesei.

Mello-de-Sousa TM, Rassinger A, Pucher ME, dos Santos Castro L, Persinoti GF, Silva-Rocha R, Poças-Fonseca MJ, Mach RL, Nascimento Silva R, Mach-Aigner AR.

BMC Genomics. 2015 Aug 7;16:588. doi: 10.1186/s12864-015-1807-7.


Comparative analyses of downstream signal transduction targets modulated after activation of the AT1 receptor by two β-arrestin-biased agonists.

Santos GA, Duarte DA, Parreiras-E-Silva LT, Teixeira FR, Silva-Rocha R, Oliveira EB, Bouvier M, Costa-Neto CM.

Front Pharmacol. 2015 Jul 1;6:131. doi: 10.3389/fphar.2015.00131. eCollection 2015.


Development of New Modular Genetic Tools for Engineering the Halophilic Archaeon Halobacterium salinarum.

Silva-Rocha R, Pontelli MC, Furtado GP, Zaramela LS, Koide T.

PLoS One. 2015 Jun 10;10(6):e0129215. doi: 10.1371/journal.pone.0129215. eCollection 2015.


The pWW0 plasmid imposes a stochastic expression regime to the chromosomal ortho pathway for benzoate metabolism in Pseudomonas putida.

Silva-Rocha R, de Lorenzo V.

FEMS Microbiol Lett. 2014 Jul;356(2):176-83. doi: 10.1111/1574-6968.12400.


Defining the genome-wide role of CRE1 during carbon catabolite repression in Trichoderma reesei using RNA-Seq analysis.

Antoniêto AC, dos Santos Castro L, Silva-Rocha R, Persinoti GF, Silva RN.

Fungal Genet Biol. 2014 Dec;73:93-103. doi: 10.1016/j.fgb.2014.10.009. Epub 2014 Oct 18.


Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening.

Guazzaroni ME, Silva-Rocha R, Ward RJ.

Microb Biotechnol. 2015 Jan;8(1):52-64. doi: 10.1111/1751-7915.12146. Epub 2014 Aug 13. Review.


Expanding the logic of bacterial promoters using engineered overlapping operators for global regulators.

Guazzaroni ME, Silva-Rocha R.

ACS Synth Biol. 2014 Sep 19;3(9):666-75. doi: 10.1021/sb500084f. Epub 2014 Jul 28.


Deciphering the cis-regulatory elements for XYR1 and CRE1 regulators in Trichoderma reesei.

Silva-Rocha R, Castro Ldos S, Antoniêto AC, Guazzaroni ME, Persinoti GF, Silva RN.

PLoS One. 2014 Jun 18;9(6):e99366. doi: 10.1371/journal.pone.0099366. eCollection 2014.


Chromosomal integration of transcriptional fusions.

Silva-Rocha R, de Lorenzo V.

Methods Mol Biol. 2014;1149:479-89. doi: 10.1007/978-1-4939-0473-0_37.


Comparative metabolism of cellulose, sophorose and glucose in Trichoderma reesei using high-throughput genomic and proteomic analyses.

Dos Santos Castro L, Pedersoli WR, Antoniêto ACC, Steindorff AS, Silva-Rocha R, Martinez-Rossi NM, Rossi A, Brown NA, Goldman GH, Faça VM, Persinoti GF, Silva RN.

Biotechnol Biofuels. 2014 Mar 21;7(1):41. doi: 10.1186/1754-6834-7-41.


The differential response of the Pben promoter of Pseudomonas putida mt-2 to BenR and XylS prevents metabolic conflicts in m-xylene biodegradation.

Pérez-Pantoja D, Kim J, Silva-Rocha R, de Lorenzo V.

Environ Microbiol. 2015 Jan;17(1):64-75. doi: 10.1111/1462-2920.12443. Epub 2014 Apr 2.


Expression pattern of cellulolytic and xylanolytic genes regulated by transcriptional factors XYR1 and CRE1 are affected by carbon source in Trichoderma reesei.

Castro Ldos S, Antoniêto AC, Pedersoli WR, Silva-Rocha R, Persinoti GF, Silva RN.

Gene Expr Patterns. 2014 Mar;14(2):88-95. doi: 10.1016/j.gep.2014.01.003. Epub 2014 Jan 27.


The private life of environmental bacteria: pollutant biodegradation at the single cell level.

Nikel PI, Silva-Rocha R, Benedetti I, de Lorenzo V.

Environ Microbiol. 2014 Mar;16(3):628-42. doi: 10.1111/1462-2920.12360. Epub 2014 Jan 16. Review.


Transcriptomic fingerprinting of Pseudomonas putida under alternative physiological regimes.

Kim J, Oliveros JC, Nikel PI, de Lorenzo V, Silva-Rocha R.

Environ Microbiol Rep. 2013 Dec;5(6):883-91. doi: 10.1111/1758-2229.12090. Epub 2013 Sep 5.


Engineering multicellular logic in bacteria with metabolic wires.

Silva-Rocha R, de Lorenzo V.

ACS Synth Biol. 2014 Apr 18;3(4):204-9. doi: 10.1021/sb400064y. Epub 2013 Jul 22.


Quantitative, non-disruptive monitoring of transcription in single cells with a broad-host range GFP-luxCDABE dual reporter system.

Benedetti IM, de Lorenzo V, Silva-Rocha R.

PLoS One. 2012;7(12):e52000. doi: 10.1371/journal.pone.0052000. Epub 2012 Dec 28.


The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes.

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.

Nucleic Acids Res. 2013 Jan;41(Database issue):D666-75. doi: 10.1093/nar/gks1119. Epub 2012 Nov 23.


The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space.

Silva-Rocha R, de Lorenzo V.

Environ Microbiol. 2013 Jan;15(1):271-86. doi: 10.1111/1462-2920.12014. Epub 2012 Nov 22.


Decoding the genetic networks of environmental bacteria: regulatory moonlighting of the TOL system of Pseudomonas putida mt-2.

Silva-Rocha R, Pérez-Pantoja D, de Lorenzo V.

ISME J. 2013 Feb;7(2):229-32. doi: 10.1038/ismej.2012.98. Epub 2012 Aug 16. No abstract available.


Stochasticity of TOL plasmid catabolic promoters sets a bimodal expression regime in Pseudomonas putida mt-2 exposed to m-xylene.

Silva-Rocha R, de Lorenzo V.

Mol Microbiol. 2012 Oct;86(1):199-211. doi: 10.1111/j.1365-2958.2012.08184.x. Epub 2012 Aug 16.

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