The Antiviral Response in Plants: RNA Silencing Melissa Andreas Carrington Lab HHMI - Oregon State University Summer 2007.

Slides:

Advertisements

Similar presentations

Dogmatic View of Gene Expression DNAProteinRNA Post-transcriptional Control: Quantitative Control: Levels of mRNA not proportional to levels of mRNA synthesized.

Advertisements

Identification of the Plant Systemic RNA Silencing Signal 2008 Summer HHMI Program Simon Johnson Mentors: Dr. James C. Carrington – Professor and Director.

Emi Birch, Lilly Hoff, Julia Kuczkowski, Lucas Stover Arabidopsis thaliana – the Effects of pH on RDR6 and DCL4 Mutants Steamboat Springs High School Throughout.

Dicer-Like A RNA Helicase Gene Involved in Gene Silencing UCSF Max BachourJessica ChenChris McQuilkin.

By: Kristin Watkins, Lindsay Baum, and Kylie Dickson

TuMV, miRNAs and Arabidopsis thaliana Amy Shatswell HHMI Summer Research 2006 Carrington Lab.

Phytophthora Small RNA Database: Visualization of Small RNAs Using a Genome Viewer Deepthika Ennamuri Mentor: Dr. Niklaus J. Grünwald REU Summer 2011 Internship.

Viral and Cellular MicroRNAs as Determinants of Viral Pathogenesis and Immunity Role of miRNAs in interaction between viruses and their hosts Ines Hahn,

RNA Interference (RNAi) Pathway

Comparison of microRNA populations in SACMV infected tolerant and susceptible cassava landraces 9 th Regional Plant Biotechnology Forum.

Functional consequences of NLS mutations in human MLH1 Alex Dukes Dr. Andrew Buermeyer Department of Environmental & Molecular Toxicology Oregon State.

Advantages of C. elegans: 1. rapid life cycle 2. hermaphrodite

Specificity of argonaute protein association with miRNA Molly Blatz Dr. Jim Carrington Dr. Sunny Gilbert.

Role of Arabidopsis RNA- Dependent RNA Polymerase Genes 3, 4 and 5 in Antiviral Defense Nick Lowery Dr. James C. Carrington Dr. Hernan Garcia-Ruiz Oregon.

Andres Alvarez Dr. Jeff Chang IDENTIFICATION OF CANDIDATE TARGET PROTEINS OF TYPE III EFFECTORS.

Translational Inhibition in Arabidopsis thaliana Russell Burke Dr. James Carrington Botany and Plant Pathology.

MicroRNA in Developing and Germinating Arabidopsis thaliana Seeds Jing Sun Mentor: Dr. Hiro Nonogaki.

USDA National Institute of Food & Agriculture Grant created to fund late blight control Caused by Phytophthora infestans Species of Oomycete (water molds)

Production of Turnip yellow mosaic virus Capsids: The Future in Micronutrient Delivery Nicole Dzialowy Dr. Yannis Tzanetakis Dr. Theo Dreher Department.

Can RNA form base pairs? Yes, in many circumstances Some are strictly dsRNA molecules, others are folded back pieces of ssRNA with interactions between.

Virus-host interactions

Establishment of a System to Replicate, Purify, and Use a Mutant RNA Virus to Study the Antiviral Defense Response in Plants Katie Brempelis Mentors: Dr.

Identifying Genes in E. coli Required for Susceptibility to Antisense Antibiotics Susan Puckett Mentor: Dr. Bruce Geller AVI BioPharma Howard Hughes Medical.

The Small RNA World

RNAi. What is RNAi? RNA-based mechanisms of gene silencing. These siRNAs are bound by a protein-RNA complex called the RNA-induced silencing complex (RISC)

Transfection. What is transfection? Broadly defined, transfection is the process of artificially introducing nucleic acids (DNA or RNA) into cells, utilizing.

BEH. 109: Laboratory Fundamentals in Biological Engineering

RNA interference Definition: RNA interference (RNAi) is a mechanism where the presence of certain fragments.

MBP1007/ Nucleic Acids A functional mRNA: The cytoplasmic story Objectives (1) To discuss the iNUTS and iBOLTS of how mRNAs function in the cytoplasm.

SiRNA and Epigenetic Asma Siddique Saloom Aslam Syeda Zainab Ali.

rasiRNAs: a class of small regulatory RNAs

Changes to Syllabus: Quizzes put back: Change Oct. 3 to Oct. 17

RNA interference: Kill the messenger!. conclusion: dsRNA triggers potent and specific gene silencing inject worms with dsRNA corresponding to.

Carly Sproule BE  Mechanism that silences a gene so that the protein associated with it is not expressed  Regulates gene expression  Used as.

Epigenetics: RNAi and Heterochromatin formation

Welcome Everyone. Self introduction Sun, Luguo ( 孙陆果） Contact me by Professor in School of Life Sciences & National Engineering.

Arabidopsis thaliana Response to Tobacco Rattle Virus Jessica Martin, Cory Zoetewey, and Lisa K. Johansen, Department of Biology University of Colorado.

Youngae Lee Identification of microRNA function by target prediction and expression profiling.

The Role of the Actin Cytoskeleton in Plant/Pathogen Interactions Meesha Peña Dr. Jeff Chang Botany and Plant Pathology.

Characterization of RDR Gene Expression Johnny R. Nunez and Lisa K. Johansen Community College of Denver and University of Colorado at Denver and Health.

Nature, 2008, Doi: /nature07103 Semrah Kati

The Power of “Genetics” LOSS OF FUNCTION Easy in yeast Difficult in mammals Powerful tool to address roles in developmental or signaling networks Gene.

Trumpet leaves and microRNA Catherine Kidner CSHL.

RNA-ligand interactions and control of gene expression

RNA silencing as an immune system in plants

microRNA mediated host-virus interactions

Viral Silencing Suppressors. Tools forged to fine-tune host-pathogen coexistence.

Vectors for RNAi.

Atta ur Rahman school of biological Science National University of Sciences & Technology CMB-234:Molecular Biology.

Ch 16. Posttranscriptional Regulation RNA interference (RNAi)

Viruses A “borrowed life”. Characteristics of Life All living things exhibit the following four characteristics: 1.Carry out metabolic activities to meet.

Mestrado Integrado em Medicina Biologia Celular e Molecular II

An Introduction to RNA Interference

Figure 1. RISC activity in BYL. ( A ) Quantity of AGO1 protein in BYL

I Virus e l’RNAi approfondimenti.

Using artificial microRNAs to induce Cassava Brown Streak Disease resistance in cassava Henry Wagaba.

The plant Mediator and its role in noncoding RNA production

Biochemical Specialization within Arabidopsis RNA Silencing Pathways

Short interfering RNA siRNA

Short interfering RNA siRNA

Damien Garcia, Shahinez Garcia, Olivier Voinnet Cell Host & Microbe

Short interfering RNA siRNA

Antiviral RNA-induced silencing complexes

Edwards Allen, Zhixin Xie, Adam M. Gustafson, James C. Carrington Cell

Volume 4, Issue 2, Pages (February 2003)

Antiviral RNA Silencing in Mammals: No News Is Not Good News

Antiviral Immunity Directed by Small RNAs

Ancient Endo-siRNA Pathways Reveal New Tricks

A Counterdefensive Strategy of Plant Viruses

Presentation transcript:

The Antiviral Response in Plants: RNA Silencing Melissa Andreas Carrington Lab HHMI - Oregon State University Summer 2007

Plants and Pathogens 15% of worldwide food production is lost to pathogens Viruses cause est. $60 billion per year in crop damages Antiviral mechanisms in plants are not fully understood Garcia-Arenal et.al. (1996) Phytopathology 86: 535

Mechanisms of Defense Innate immunity: quarantine of infected cells Not pathogen-specific Adaptive response: RNA silencing Triggered by invading nucleic acids Response tailored to the pathogen

Project Goals To characterize the antiviral silencing response in a model organism Infected: Uninfected Turnip mosaic virus Lellis et. al. (2002) Curr.Biol.12: Arabidopsis and Turnip Mosaic Virus (TuMV-GFP) Collect and sequence small RNA Identify origin of RNA Describe small RNA population

Viral Accumulation Day 5 Day 6 Day 7 Control Day 1 Day 2 Day 3 Day 4 Control

Viral Accumulation Is TuMV targeted by RNA silencing in Arabidopsis?

RNA Silencing Basics Mechanism of degrading specific sequences of RNA Used mainly for antiviral defense and gene regulation

RNA Silencing Mechanism Double-stranded RNA Degraded target Target RNA Target AGO siRNA * RISC AGO Dicer RDR

Dicers and Arabidopsis Four kinds of Dicer-like (DCL) proteins in Arabidopsis Specialization: nucleotide length and task DCL 1: 21 nt – microRNAs DCL 2: nt – various DCL 3: 24 nt – heterochromatin formation DCL 4: 21 nt – post-transcriptional silencing Antiviral roles are unknown Double-stranded RNA Degraded target Target RNA Target AGO Dicer

Experimental Setup Arabidopsis plants infected with Turnip Mosaic Virus (TuMV-GFP) Mock-infected control plants Time points: 7 and 10 days post-infection (dpi) DCL mutants: dcl1-7 and dcl2 dcl3 dcl4 triple mutant

TuMV-GFP Genome Comparison Region of Genome Shown small RNA arising from this region of viral RNA Diagram of Viral RNA

Virus-Derived Small RNA in Dicer Mutants Reads derived from the Arabidopsis genome Reads derived from the TuMV-GFP genome

Viral RNA in Dicer Mutants dcl 1-7dcl 234 dcl 1-7 dcl 234

Conclusion Turnip Mosaic Virus is a target of RNA silencing in Arabidopsis.

The Next Step Infect with a TuMV-GFP suppressor mutant Expand to other Dicer mutants dcl2 dcl4 Examine the dynamics of small RNA production

Acknowledgments Funding: Howard Hughes Medical Institute Dr. Kevin Ahern Mentors: Elisabeth Chapman Kristin Kasschau Jim Carrington