1
|
Mills A, Jaganatha V, Cortez A, Guzman M, Burnette JM, Collin M, Lopez-Lopez B, Wessler SR, Van Norman JM, Nelson DC, Rasmussen CG. A Course-Based Undergraduate Research Experience in CRISPR-Cas9 Experimental Design to Support Reverse Genetic Studies in Arabidopsis thaliana. J Microbiol Biol Educ 2021; 22:e00155-21. [PMID: 34594454 PMCID: PMC8442021 DOI: 10.1128/jmbe.00155-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Gene-editing tools such as CRISPR-Cas9 have created unprecedented opportunities for genetic studies in plants and animals. We designed a course-based undergraduate research experience (CURE) to train introductory biology students in the concepts and implementation of gene-editing technology as well as develop their soft skills in data management and scientific communication. We present two versions of the course that can be implemented with twice-weekly meetings over a 5-week period. In the remote-learning version, students performed homology searches, designed guide RNAs (gRNAs) and primers, and learned the principles of molecular cloning. This version is appropriate when access to laboratory equipment or in-person instruction is limited, such as during closures that have occurred in response to the COVID-19 pandemic. In person, students designed gRNAs, cloned CRISPR-Cas9 constructs, and performed genetic transformation of Arabidopsis thaliana. Students learned how to design effective gRNA pairs targeting their assigned gene with an 86% success rate. Final exams tested students' ability to apply knowledge of an unfamiliar genome database to characterize gene structure and to properly design gRNAs. Average final exam scores of ∼73% and ∼84% for in-person and remote-learning CUREs, respectively, indicated that students met learning outcomes. The highly parallel nature of the CURE makes it possible to target dozens to hundreds of genes, depending on the number of sections. Applying this approach in a sensitized mutant background enables focused reverse genetic screens for genetic suppressors or enhancers. The course can be adapted readily to other organisms or projects that employ gene editing.
Collapse
Affiliation(s)
- Alison Mills
- Biochemistry and Molecular Biology Graduate Program, University of California, Riverside, California, USA
| | - Venkateswari Jaganatha
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Alejandro Cortez
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Michael Guzman
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - James M. Burnette
- College of Natural and Agricultural Sciences, University of California, Riverside, California, USA
| | - Matthew Collin
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Berenise Lopez-Lopez
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Susan R. Wessler
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Jaimie M. Van Norman
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - David C. Nelson
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Carolyn G. Rasmussen
- Biochemistry and Molecular Biology Graduate Program, University of California, Riverside, California, USA
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| |
Collapse
|
2
|
Garud A, Carrillo AJ, Collier LA, Ghosh A, Kim JD, Lopez-Lopez B, Ouyang S, Borkovich KA. Genetic relationships between the RACK1 homolog cpc-2 and heterotrimeric G protein subunit genes in Neurospora crassa. PLoS One 2019; 14:e0223334. [PMID: 31581262 PMCID: PMC6776386 DOI: 10.1371/journal.pone.0223334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/18/2019] [Indexed: 11/19/2022] Open
Abstract
Receptor for Activated CKinase-1 (RACK1) is a multifunctional eukaryotic scaffolding protein with a seven WD repeat structure. Among their many cellular roles, RACK1 homologs have been shown to serve as alternative Gβ subunits during heterotrimeric G protein signaling in many systems. We investigated genetic interactions between the RACK1 homolog cpc-2, the previously characterized Gβ subunit gnb-1 and other G protein signaling components in the multicellular filamentous fungus Neurospora crassa. Results from cell fractionation studies and from fluorescent microscopy of a strain expressing a CPC-2-GFP fusion protein revealed that CPC-2 is a cytoplasmic protein. Genetic epistasis experiments between cpc-2, the three Gα genes (gna-1, gna-2 and gna-3) and gnb-1 demonstrated that cpc-2 is epistatic to gna-2 with regards to basal hyphae growth rate and aerial hyphae height, while deletion of cpc-2 mitigates the increased macroconidiation on solid medium observed in Δgnb-1 mutants. Δcpc-2 mutants inappropriately produce conidiophores during growth in submerged culture and mutational activation of gna-3 alleviates this defect. Δcpc-2 mutants are female-sterile and fertility could not be restored by mutational activation of any of the three Gα genes. With the exception of macroconidiation on solid medium, double mutants lacking cpc-2 and gnb-1 exhibited more severe defects for all phenotypic traits, supporting a largely synergistic relationship between GNB-1 and CPC-2 in N. crassa.
Collapse
Affiliation(s)
- Amruta Garud
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Alexander J. Carrillo
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Logan A. Collier
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Arit Ghosh
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - James D. Kim
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Berenise Lopez-Lopez
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Shouqiang Ouyang
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Katherine A. Borkovich
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
- * E-mail:
| |
Collapse
|