Contreras Lab

About The Contreras Lab

The Contreras Lab's research combines biomolecular engineering, genetic studies and computational modeling to understand molecular features that lead to the specific recognition and interaction of regulatory RNAs and proteins. They apply fundamental concepts that emerge from experimental (and computational) work to develop novel applications that could beneficially impact human health and biotechnology. Overall research interests:

• Transcriptional regulation
• Regulatory RNA networks
• Epitranscriptomics
• RNA-protein interactions and RNA-protein folding
• Novel molecular tools for intracellular studies of RNA-metabolism
• Diagnostics for RNA-related diseases
• Molecular mechanisms of stress-responses

2023 Research

• Miller LG, Demny M, Tamamis P, Contreras LM. Characterization of epitranscriptome reader proteins experimentally and in silico: Current knowledge and future perspectives beyond the YTH domain. Comput Struct Biotechnol J. 2023 Jun 30;21:3541-3556. PMID: 37501707; PMCID: PMC10371769.

• Buchser R, Sweet P, Anantharaman A, Contreras L. RNAs as Sensors of Oxidative Stress in Bacteria. Annu Rev Chem Biomol Eng. 2023 Jun 8;14:265-281. PMID: 37289561.

  Sweet P, Blacutt J, Gordon V, Contreras L. Exposure of Shewanella oneidensis MR-1 to Sublethal Doses of Ionizing Radiation Triggers Short-Term SOS Activation and Longer-Term Prophage Activation. Appl Environ Microbiol. 2023 Mar 29;89(3):e0171622. Epub 2023 Feb 27. PMID: 36847540; PMCID: PMC10057963.

2022 Research

• Han R, Jiang J, Fang J, Contreras LM. PNPase and RhlB Interact and Reduce the Cellular Availability of Oxidized RNA in Deinococcus radiodurans. Microbiol Spectr. 2022 Aug 31;10(4):e0214022.  Epub 2022 Jul 20. PMID: 35856907; PMCID: PMC9430589.

• Hillsley A, Santoso MS, Engels SM, Halwachs KN, Contreras LM, Rosales AM. A strategy to quantify myofibroblast activation on a continuous spectrum. Sci Rep. 2022 Jul 18;12(1):12239. PMID: 35851602; PMCID: PMC9293987.

• Ekdahl AM, Rojano-Nisimura AM, Contreras LM. Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria. J Mol Biol. 2022 Sep 30;434(18):167689. Epub 2022 Jun 16. PMID: 35717997.

• Simmons TR, Ellington AD, Contreras LM. RNP-Based Control Systems for Genetic Circuits in Synthetic Biology Beyond CRISPR. Methods Mol Biol. 2022;2518:1-31.  PMID: 35666436.

• A Hillsley, M Santoso, SM Engels, LM Contreras, and AM Rosales. A Strategy to Quantify Myofibroblast Activation on a Continuous Spectrum. (Submitted). Biorxiv. Preprint. March 11, 2022.

2021 Research

• A Leistra, M Mihailovic, A Rojano Nisimura, T Simmons, I Joseph, N Curtis, and LM Contreras. CsrA Interacts With sRNA Regulatory Networks. (Submitted). 2021.

• MR Burroughs, JC Gonzalez-Rivera, A Cordova, and LM Contreras. Experimental and Computational Methods for Guiding Identification and Characterization of Epitranscriptome Proteins. RNA Technologies 593–632. July 29, 2021. 

• A Chen, J Hernández-Vargas, R Han, O Cortazar-Martínez, N Gonzalez, S Patel, B Keitz, G Luna-Barcenas, and LM Contreras. Small RNAs as a New Platform for Tuning the Biosynthesis of Silver Nanoparticles for Enhanced Material and Functional Properties. ACS Applied Materials & Interfaces. July 28, 2021.

• M Mihailovic, A Ekdahl, A Chen, A Leistra, B Li, J González Martínez, M Law, C Ejindu, É Massé, P Freddolino and LM Contreras. Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study. Frontiers in Cellular and Infection Microbiology 11, 696533. July 13, 2021.

• JK Villa, R Han, C-H Tsai, A Chen, P Sweet, G Franco, R Vaezian, R Tkavc, MJ Daly and LM Contreras. A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation. Scientific Reports 11, 12949. June 21, 2021. 

• M Sherman, S Sandeep, and LM Contreras. The Tryptophan-Induced tnaC Ribosome Stalling Sequence Exposes High Amino Acid Cross-Talk That Can Be Mitigated by Removal of NusB for Higher Orthogonality. ACS Synthetic Biology. April 9, 2021.

2020 Research

• R Han, J Fang, J Jiang, EK Gaidamakova, R Tkavc, MJ Daly and LM Contreras. Signal Recognition Particle RNA Contributes to Oxidative Stress Response in Deinococcus radiodurans by Modulating Catalase Localization. Frontiers in Microbiology 11, 613571. December 18, 2020

• Lukasiewicz, A and LM Contreras. Antisense probing of dynamic RNA structures. Methods. November 2020.

• JC Gonzalez-Rivera, MW Sherman, DS Wang, JCL Chuvalo-Abraham, L Hildebrandt Ruiz, and LM Contreras. RNA oxidation in chromatin modification and DNA-damage response following exposure to formaldehyde. Scientific Reports 10, 16545. October 6, 2020.

• AJ Gimenez, F Medellin-Rodriguez, LM Contreras, JM Lopez-Romero, I Sanchez, F Villasenor-Ortega, G Luna-Barcenas. Turbidimetry by image degradation analysis. IEEE Transactions on Instrumentation and Measurement. October 2020.

• LM Contreras, JC Gonzalez-Rivera, KC Baldridge, DS Wang, JCL. Chuvalo-Abraham, and L Hildebrandt Ruiz. Understanding the Functional Impact of VOC-Ozone Mixtures on the Chemistry of RNA in Epithelial Lung Cells. Res Rep Health Eff Inst, (201):201. July 2020.

• JC Gonzalez-Rivera, KC Baldridge, DS Wang, KH Patel, JCL. Chuvalo-Abraham, L Hildebrandt Ruiz, and LM Contreras. Post-transcriptional air pollution oxidation to the cholesterol biosynthesis pathway promotes pulmonary stress phenotypes. Communications Biology 3, 392. July 22, 2020.

• R Han, K Haning, JC Gonzalez-Rivera, Y Yang,  R Li, S-H Cho, J Huang, B Simonsen, S Yang, LM Contreras. Multiple small RNAs interact to co-regulate ethanol tolerance in Zymomonas mobilis. Frontiers in Bioengineering and Biotechnology, 8. March 4, 2020. 

• EK Bowman, MK Mihailovic, B Li, and LM Contreras. Bioinformatic Application of Fluorescence-based in vivo RNA Regional Accessibility Data to Identify Novel sRNA Targets. In: Arluison V., Wien F. (eds) RNA Spectroscopy. Methods in Molecular Biology, vol 2113. Humana, New York, NY. February 1, 2020. 

• JC Gonzalez-Rivera, AA Orr, SM Engels, JM Jakubowski, MW Sherman, KN O’Connor, T Matteson, BC Woodcock, LM Contreras and P Tamamis. Computational evolution of an RNA-binding protein towards enhanced oxidized RNA binding. Computational and Structural Biotechnology Journal, 28:137-152. 2020. 

• K Haning, SM Engels, P Williams, M Arnold, and LM Contreras. Applying a new REFINE approach in Zymomonas mobilis identifies novel sRNAs that confer improved stress tolerance phenotypes. Frontiers in Microbiology. January 10, 2020.