Bonilla Lab
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Bonilla lab at University
​of San Diego 

Stress is a fact of life for bacteria in a dynamic environment. My lab focuses on the general stress response sigma factor, SigB, and its role in cell physiology. B. subtilis uses the stressosome, a multiprotein complex, to sense its environment and RsbPQ to sense energy stress.  We are interested in teasing out the role of these SigB regulatory proteins during stress, the molecular interactions that control their activities, and the cellular functions responsible for the physiological response during stress. We approach these questions using genetics, bioinformatics, molecular and microbiology techniques. Our findings will elucidate the genetic and molecular determinants of bacterial resilience. ​

Research

​We study the bacterial response to environmental stress and the role of the general stress sigma factor SigB in protection against this stress. We use classical microbial physiology assays, genetic, molecular, cellular and biochemical techniques to understand SigB regulation and its targets. We ask the following:
What are the cellular functions of SigB targets that help cells survive stress?
How does SigB and the regulatory signaling proteins contribute to antioxidant properties of bacteria?

Publications/ In the news

Microbe 2022 ASM meeting symposium. Culturally Relevant Microbiology Education. https://asm.org/Articles/2022/July/From-Classrooms-to-Labs-Social-Equity-in-Microbiol

Cultivating an Equity-Focused Classroom. American Society for Microbiology (2021).  https://asm.org/Articles/2021/November/Cultivating-an-Equity-Focused-Classroom
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Hoai Tran and Carla Y. Bonilla. SigB-regulated antioxidant functions in Gram-positive bacteria: potentials for medical and environmental applications. World Journal of Microbiology and Biotechnology (2021). https://rdcu.be/ceRK2
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Carla Y Bonilla, Generally stressed out bacteria: environmental stress response mechanisms in Gram-positive bacteria, Integrative and Comparative Biology (2020) icaa002, https://academic.oup.com/icb/article/60/1/126/5733733?guestAccessKey=87f285e1-f2dc-4db0-afc4-7a25a18509d3

Tran V, Geraci K, Midili G, Satterwhite W, Wright R and Bonilla CY. Resilience to oxidative and nitrosative stress is mediated by the stressosome, RsbP and SigB in Bacillus subtilis. J Basic Microbiol (2019) https://doi.org/10.1002/jobm.201900076
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Bonilla CY and Grossman AD. The primosomal protein DnaD inhibits cooperative DNA binding by the replication initiator DnaA in Bacillus subtilis (2012) Journal of Bacteriology 194(18) 5110-7 . https://jb.asm.org/content/194/18/5110.long

Smits WK, Merrikh H, Bonilla CY and Grossman AD. Primosomal proteins DnaD and DnaB are recruited to chromosomal regions bound by DnaA in Bacillus subtilis (2011) Journal of Bacteriology 193(3):640-8.  https://jb.asm.org/content/193/3/640.long

Bonilla CY, Melo J. A., and Toczyski, D. P. Co-localization of sensors is sufficient to activate the DNA damage checkpoint in the absence of damage. (2008) Molecular Cell 30, 267-276.

Vidanes G., Bonilla CY, Toczyski D. P. Complicated Tails: Chromatin remodeling and the DNA damage response (2005) Cell 121, 973-976.

Cao M, Salzberg L, Tsai CS, Mascher T, Bonilla C, Wang T, Ye RW, Marquez-Magana L, Helmann JD. Regulation of the Bacillus subtilis extracytoplasmic function protein sigma (Y) and its target promoters. (2003) Journal of Bacteriology 185, 4883-4890.

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Student Presentations

Subtillery Virtual International Conference, 2021. Talk. Assessing membrane fluidity in Bacillus subtilis during oxidative stress. Andrew Jimenez. 

Murdock College Science Research Conference, 2020. Virtual Poster. Phylogenomic analysis of RsbQ alpha/beta hydrolase cellular function during energy stress in Bacillus subtilis. Duc M Hoang.
Murdock College Research Science Conference, 2018. Poster. Contribution of ydaD, a NADH-dependent dehydrogenase, to oxidative stress resistance of Bacillus subtilis. Hoai Tran.

ZagFam Weekend, Gonzaga University, 2018. Poster. Transcriptional regulation of the ydaD gene in Bacillus subtilis in the presence of reactive oxygen species. Erika Santacuz.


Society for the Advancement of Chicanos/Hispanics and Native Americans in Science, 2017. Elucidating the activation mechanism of the transcription factor SigmaB when Bacillus subtilis is exposed to reactive oxygen species. Erika Santacruz. Poster

Murdock College Research Science Conference, 2017. Testing the ability of Bacillus subtilis to cross protect against oxidative stress. Vina Tran. Poster.

Molecular Genetics of Bacteria and Phage Meeting, 2016. Testing the sufficiency of the stressosome protein RsbRA in the oxidative stress response of Bacillus subtilis. Vina Tran. Poster. 
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Microbe, American Society for Microbiology, Boston, 2016. Testing the composition of the Bacillus subtilis stressosome complex using co-immunoprecipitation in vivo. Karina Lopez-Damian. Poster.

Murdock College Research Science Conference, 2015. The role of the stressosome in the H2O2 stress response of Bacillus subtilis Kara Geraci. Talk
 
Gonzaga Fall Family Weekend, 2015. Testing the genetic requirement of stressosome genes in the H2O2 stress response in Bacillus subtilis. Kara Geraci and Giovanni Midili. Poster.
 
Molecular Genetics of Bacteria and Phage Meeting, 2015. Examination of the Bacillus subtilis stressosome in vivo in the presence of stress. Karina Lopez-Damian. Poster
 
Murdock College Research Science Conference, 2014. Visualizing YtvA Protein Levels During Disulfide Stress in Bacillus subtilis, Paige Nienjuis. Poster
 
Gonzaga Fall Family Weekend, 2014. The role of the stressosome in the oxidative stress response pathway of Bacillus subtilis, Nico Cunanan, Paige Nieunhuis, Giovanni Midili. Poster
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