Biology subjects

Gendron, J. M.

Publications and source records attributed to Gendron, J. M..

7 recordsLinked to original sources

bioRxiv2023

The circadian clock regulates PIF3 protein stability in parallel to red light

The circadian clock is an endogenous oscillator, but its importance lies in its ability to impart rhythmicity on downstream biological processes or outputs. Focus has been placed on understanding the core transcription factors of the circadian clock and how they connect to outputs through regulated gene transcription. However, far less is known about posttranslational mechanisms that tether clocks to output processes through protein regulation. Here, we identify a protein degradation mechanism that tethers the clock to photomorphogenic growth. By performing a reverse genetic screen, we identify a clock-regulated F-box type E3 ubiquitin ligase, CLOCK-REGULATED F-BOX WITH A LONG HYPOCOTYL 1 (CFH1), that controls hypocotyl length. We then show that CFH1 functions in parallel to red light signaling to target the transcription factor PIF3 for degradation. This work demonstrates that the circadian clock is tethered to photomorphogenesis through the ubiquitin proteasome system and that PIF3 protein stability acts as a hub to integrate information from multiple environmental signals.

plant biology↗

bioRxiv2022

Diverse photoperiodic gene expression patterns are likely mediated by distinct transcriptional systems in Arabidopsis

Photoperiod is an annual cue measured by biological systems to align growth and reproduction with the seasons. In plants, photoperiodic flowering has been intensively studied for over 100 years, but we lack a complete picture of the transcriptional networks and cellular processes that are photoperiodic. We performed a transcriptomics experiment on Arabidopsis plants grown in 3 different photoperiods, and find that nearly one-third of the known genes show photoperiodic alteration in gene expression. Gene clustering, daily expression integral calculations and cis-element analysis then separate photoperiodic genes into co-expression subgroups that display 19 diverse seasonal expression patterns, opening the possibility that many photoperiod measurement systems work in parallel in Arabidopsis. Then, functional enrichment analysis predicts co-expression of important cellular pathways. To test these predictions, we generated a comprehensive catalog of genes in the phenylpropanoid biosynthesis pathway, overlaid gene expression data and demonstrated that photoperiod intersects with the two major phenylpropanoid pathways differentially, controlling flavonoids but not lignin. Finally, we describe the development of a new app that visualizes photoperiod transcriptomic data for the wider community.

plant biology↗

bioRxiv2022

Sugar sensation and mechanosensation in the egg-laying preference shift of Drosophila suzukii

The agricultural pest Drosophila suzukii differs from most other Drosophila species in that it lays eggs in ripe, rather than overripe, fruit. Previously we showed that changes in bitter taste sensation accompanied this adaptation (Dweck et al., 2021). Here we show that D. suzukii has also undergone a variety of changes in sweet taste sensation. D. suzukii has a weaker preference than D. melanogaster for laying eggs on substrates containing all three primary fruit sugars: sucrose, fructose, and glucose. Major subsets of D. suzukii taste sensilla have lost electrophysiological responses to sugars. Expression of several key sugar receptor genes is reduced in the taste organs of D. suzukii. By contrast, certain mechanosensory channel genes, including nompC, are expressed at higher levels in the taste organs of D. suzukii, which has a higher preference for stiff substrates. Finally, we find that D. suzukii responds differently from D. melanogaster to combinations of sweet and mechanosensory cues. Thus, the two species differ in sweet sensation, mechanosensation, and their integration, which are all likely to contribute to the differences in their egg-laying preferences in nature.

neuroscience↗

bioRxiv2020

A WD40 repeat-like protein pathway connects F-BOX STRESS INDUCED (FBS) proteins to the NIGT1.1 transcriptional repressor in Arabidopsis

SCF-type E3 ubiquitin ligases use F-box (FBX) proteins as interchangeable substrate adaptors to recruit protein targets for ubiquitylation. FBX proteins almost universally have structure with two domains. A conserved N-terminal F-box domain interacts with a SKP protein and connects the FBX protein to the core SCF complex, while a C-terminal domain interacts with the protein target and facilitates recruitment. The F-BOX STRESS INDUCED (FBS) subfamily of four plant FBX proteins has atypical domain structure, however, with a centrally located F-box domain and additional conserved regions at both the N- and C-termini. FBS proteins have been linked to environmental stress networks, but no ubiquitylation target(s) or exact biological function has been established for this subfamily. We have identified two WD40 repeat-like proteins in Arabidopsis that are highly conserved in plants and interact with FBS proteins, which we have named FBS INTERACTING PROTEINs (FBIPs). FBIPs interact exclusively with the N-terminus of FBS proteins, and this interaction occurs in the nucleus. FBS1 destabilizes FBIP1, consistent with FBIPs being ubiquitylation targets of SCFFBS complexes. Furthermore, we found that FBIP1 interacts with NIGT1.1, a GARP-type transcriptional repressor that regulates nitrate and phosphate starvation signaling and responses. Collectively, these interactions between FBS, FBIP, and NIGT1.1 proteins delineate a previously unrecognized SCF-connected transcription regulation module that works in the context of phosphate and nitrate starvation, and possibly other environmental stresses. Importantly, this work also identified two uncharacterized WD40 repeat-like proteins as new tools with which to probe how an atypical SCF complex, SCFFBS, functions via FBX protein N-terminal interaction events.

plant biology↗

bioRxiv2020

A Decoy Library Uncovers U-box E3 Ubiquitin Ligases that Regulate Flowering Time in Arabidopsis

Targeted degradation of proteins is mediated by E3 ubiquitin ligases and is important for the execution of many biological processes. Previously, we created and employed a large library of E3 ubiquitin ligase decoys to identify regulators of the circadian clock (Feke et al., 2019). In tandem with the screen for circadian regulators, we performed a flowering time screen using our U-box-type E3 ubiquitin ligase decoy transgenic library. We identified five U-box decoy transgenic populations that have defects in flowering time or the floral development program. We used additional genetic and biochemical studies to validate PLANT U-BOX 14 (PUB14), MOS4-ASSOCIATED COMPLEX 3A (MAC3A), and MAC3B as bona fide regulators of flowering time. This work reinforces the utility of the decoy library in identifying regulators of important developmental transitions in plants and expands the scope of the technique beyond our previous studies.

plant biology↗

bioRxiv2019

GIGANTEA recruits deubiquitylases, UBP12 and UBP13, to regulate accumulation of the ZTL photoreceptor complex

To remain synchronous with the environment, plants constantly survey daily light conditions using an array of photoreceptors and adjust their circadian rhythms accordingly. ZEITLUPE (ZTL), a blue light photoreceptor with E3 ubiquitin ligase activity, communicates end-of-day light conditions to the circadian clock. To function properly, ZTL protein must accumulate but not destabilize target clock transcription factors before dusk, while in the dark ZTL mediates degradation of target proteins. It is not clear how ZTL can accumulate to high levels in the light while its targets remain stable. Two deubiquitylating enzymes, UBIQUITIN-SPECIFIC PROTEASE 12 and UBIQUITIN-SPECIFIC PROTEASE 13 (UBP12 and UBP13), which have opposite genetic and biochemical functions to ZTL, were shown to associate with the ZTL protein complex. Here we demonstrate that the ZTL light-dependent interacting partner, GIGANTEA (GI), recruits UBP12 and UBP13 to the ZTL photoreceptor complex. We show that loss of UBP12 and UBP13 reduces ZTL and GI protein levels through a post-transcriptional mechanism. Furthermore, the ZTL target protein TOC1 is unable to accumulate to normal levels in ubp mutants, indicating that UBP12 and UBP13 are necessary to stabilize clock transcription factors during the day. Our results demonstrate that the ZTL photoreceptor complex contains both ubiquitin-conjugating and -deconjugating enzymes, and that these two opposing enzyme types are necessary for the complex to properly regulate the circadian clock. This work also shows that deubiquitylating enzymes are a core design element of circadian clocks that is conserved from plants to animals.

plant biology↗

bioRxiv2017

Decoys reveal the genetic and biochemical roles of redundant plant E3 ubiquitin ligases

The ubiquitin proteasome system (UPS) is the main cellular route for protein degradation in plants and is important for a wide range of biological processes including daily and seasonal timing. The UPS relies on the action of E3 ubiquitin ligases to specifically recognize substrate proteins and facilitate their ubiquitylation. In plants, there are three major challenges that inhibit studies of E3 ligase function: 1) rampant genetic redundancy, 2) labile interactions between an E3 ligase and its cognate substrates, and 3) a lack of tools for rapid validation of bona fide substrates. To overcome these 3 challenges, we have developed a decoy method that allows for rapid genetic analysis of E3 ligases, in vivo identification of substrates using immunoprecipitation followed by mass spectrometry, and reconstitution of the ubiquitylation reaction in mammalian cells to rapidly validate potential substrates. We employ the strategy to study the plant F-box proteins, ZTL, LKP2, and FKF1 revealing differential genetic impacts on circadian clock period and seasonal flowering. We identify a group of circadian clock transcriptional regulators that interact with ZTL, LKP2, and FKF1 in vivo providing a host of potential substrates that have not been seen previously. We then validate one substrate of ZTL, the plant circadian clock transcription factor CHE, and show that ZTL mediates CHE ubiquitylation and that the levels of the CHE protein cycle in daily timecourses. This work further untangles the complicated genetic roles of this family of E3 ligases and suggests that ZTL is a master regulator of a diverse set of critical clock transcription factors. Furthermore, the method that is validated here can be tool employed widely to overcome traditional challenges in studying redundant plant E3 ubiquitin ligases.

plant biology↗