Primary: Seth O’Conner
Characterization of PAMP-responsive Ubiquitylation in Arabidopsis
Summary of Proposal:
This proposal aims to uncover how ubiquitylation of plant-native proteins affects PAMP-Triggered Immunity (PTI). He/she gives definitions of PAMPs, Pattern recognition receptors, and gives a synopsis of the ubiquitination process (The concerted workings of E1 activating enzymes, E2 conjugating enzymes, and E3 ubiquitin ligases—E3’s being of special concern in this proposal). The author identifies PUB12 and PUB13 as E3 ubiquitin ligases which ubiquitylate FLS2 and therefore cause degradation of FLS2. They then state that much more work needs to be done to understand how ubiquitylation helps monitor PTI.
General Points:
Summary:
-In the summaryThey never explicitly state which type of proteins they will be monitoring for changes in Ubiquitylation after treatment with PAMPS. Only receptor proteins? All types of PRR proteins? Can effectors be ubiquitylated? We can assume they will be looking at all PRRs.
-The introduction does a good job of telling us what we already know about ubiquitylation/PTI and also stating what we don’t know yet. Gives us the story of PTI, common PAMP-PRR interactions, physiological responses triggered in PTI, importance of Bak1 and Bik1, what ubiquitin is, different types of ubiquitylation (mono, poly), degradation effects, common PUB E3 ubiquitin ligases and their action (and what we don’t know about them), among others.
-Introduction takes way too long to get to the objectives. It is thorough but needs to either be shortened up or rearranged so that we see the objectives more quickly.
HYPOTHESIS: “(1)PAMP-triggered ubiquitylation changes control important aspects of PTI allowing plants to restrain and fine-tune defense responses. (2) Different PAMPs trigger ubiquitylation of specific targets in addition to a core set of ubiquitylation events generated by multiple PAMPs. “
-I like their set of hypotheses and I like that it is explicitly stated. It seems to be occurring too deep into the paper. If they would have included it earlier in the summary and/or shortened their introduction it would have been better.
Objectives: (1)Analysis of FLS2-specific ubiquitylation in PAMP-triggered immunity. (2) Development of a catalog of PAMP-triggered ubiquitylation. (3) Towards an understanding of core and pattern specific ubiquitylation.
-Objectives two and three seem to be doing the same thing---they are just analyzing the data differently. Both are using the TUBE system to identify ubiquitin target proteins with various PAMP treatments. There are alternative strategies presented for objectives 1 and 2 but not objective 3 (further implicating it as the same procedure as objective two). They also state what specifically could go wrong before proposing new methods.
Overall opinions—Scientific Merit:
-This proposal is proposing something new which would advance not only the limited field of plant path interactions but also shed more light on the differing usages of ubiquitylation within plants.
-I can clearly follow all of the objectives, although the second and third one seem very similar. The introduction was rather wordy with no special importance given to any words or sentences. i.e. if an introduction is that large it might help to highlight important terms or sections.
-There are no novel techniques being used, but they provided appropriate references for research methods.
-I do believe their project will produce results and their hypothesis seem to be thought out well.
-their time allocation seems fine, there is no specifications for any collaboration. Everything will be done in lab. They continually state their labs competence in ubiquitin studies.
-Their impact was understated. Only seen in the summary and introduction: Use this information to create lines which are less susceptible to pathogens while resisting an over actve immune response. Would this be in concert with another mutation/change? In other words, it doesn’t seem like you could change an aspect in ubiquitylation which will cause both resistance and monitoring abilities. You would likely need another change as well. No significance section.