Biology subjects

Tu, Y.-T.

Publications and source records attributed to Tu, Y.-T..

4 recordsLinked to original sources

bioRxiv2025

Utilization of Arabidopsis E3 ubiquitin decoys high-throughput yeast screen platform to dissect the ubiquitin-mediated circadian clock regulation

Protein ubiquitination, mediated by E3 ubiquitin ligases, is a critical regulatory mechanism of eukaryotic cellular processes, including circadian clock function. However, identifying E3-substrate pairs remains technically challenging due to substrate instability and the genetic redundancy of E3s. To overcome these limitations, we developed a high-throughput yeast two-hybrid E3 decoy screening platform, enabling systematic mapping of E3-substrate interactions. Using a library of 283 Arabidopsis F-box and U-box E3 decoys, we screened 21 core circadian clock regulators and identified 77 potential E3-substrate interaction pairs involving 56 E3s and 16 clock proteins. Focusing on high-confidence hits, we demonstrated that PUB18 physically interacts with the central clock regulators LHY and JMJD5 and promotes their ubiquitination in planta. Genetic analyses further revealed that PUB18 and its homolog PUB19 function redundantly in circadian clock regulation. This study establishes the E3 decoy yeast two-hybrid platform as a versatile and scalable tool for dissecting ubiquitination networks in broad biological processes.

plant biology↗

bioRxiv2024

Arabidopsis EID1 E3 ubiquitin ligase regulates acquired thermotolerance by modulating HSBP translocation

Climate change is causing a rapid increase in global average temperatures and more frequent heatwaves, posing serious threats to agricultural production and global biodiversity. In response to heat stress (HS), plants can develop acquired thermotolerance (AT) by initiating a heat shock response (HSR) after mild HS priming, thereby enhancing their ability to withstand subsequent later lethal HS events. Central to this process are the HEAT SHOCK FACTORs (HSFs), which form trimeric complexes and activate the expression of HEAT SHOCK PROTEINs (HSPs) and other HSFs to maintain proper protein and cellular functionality. After heat stress subsides, the HSFs activities can be modulated to attenuate the negative effects of HSR during the heat. The SHOCK FACTOR BINDING PROTEIN (HSBP) is a conserved microprotein that plays a prominent role in modulating HSF activities. HSBP can translocate from the cytoplasm into the nucleus during heat stress to directly interact with HSFs and prevent the formation of HSF timers. However, the mechanism that regulates the HSBP cytoplasmic-nuclear shuttling remains unclear. Here, we identified an F-box E3 ubiquitin ligase, EMPFINDLICHER IM DUNKELROTEN LICHT 1 (EID1), whose mutant form shows reduced thermotolerance in AT. We showed that EID1 interacts with HSBP to modulate HSBP cytoplasm-nuclear localization during heat stress, possibly through modulating the K41 of HSBP. The decreased thermotolerance in the eid1 mutant can be explained by alterations of some HSPs expression caused by the mis-localization of HSBP. This finding provided a novel example of E3 ubiquitin-mediated regulation of heat stress in plants.

plant biology↗

bioRxiv2024

MOS4-Associated Complex subunits 3A and 3B modulate FLM splicing to repress photoperiod-dependent floral transition

Plants adjust their flowering time by integrating environmental cues through complex regulatory networks. RNA splicing plays a crucial role in modulating gene expression in response to flowering signals. The MOS4-associated complex (MAC), consisting of the evolutionarily conserved E3 ubiquitin ligases MAC3A and MAC3B, is pivotal in splicing regulation. However, their involvement in floral transition remained unclear. This study observed that mac3a/mac3b mutants flowered significantly earlier under short-day (SD) conditions, a phenotype absent under long-day (LD) conditions. This early flowering correlated with upregulation of FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) compared to wild-type plants. Transcriptomic analysis revealed alterations in transcript levels and splicing profiles of key floral regulators across different flowering pathways. Further investigation identified the thermosensory flowering regulator FLOWERING LOCUS M (FLM) as being influenced by MAC3A and MAC3B. Subsequently, we found that MAC3A and MAC3B exhibited higher expression and were associated with FLM transcripts to modulate their splicing in SD. This study elucidates how the MAC complex, through RNA splicing regulation, integrates environmental signals to modulate flowering, unveiling a new layer of complexity in flowering pathways crosstalk under non-inductive photoperiods.

plant biology↗

bioRxiv2020

The histone deacetylase HDA15 interacts with MAC3A and MAC3B to regulate intron retention of ABA-responsive genes

Histone deacetylases (HDAs) play an important role in transcriptional regulation involved in multiple biological processes. In this study, we investigate the function of HDA15 in abscisic acid (ABA) responses. Immunopurification coupled with mass spectrometry-based proteomics was used to identify the HDA15 interacting proteins. We found that HDA15 can interact with the core subunits of MOS4-Associated Complex (MAC), MAC3A and MAC3B. In addition, ABA enhances the interaction of HDA15 with MAC3B. hda15 and mac3a/mac3b mutants are ABA-insensitive in seed germination and hyposensitive to salinity. RNA sequencing (RNA-seq) analysis demonstrate that HDA15 and MAC3A/MAC3B not only affect the expression of ABA-related genes, but also regulate ABA-responsive intron retention (IR). Furthermore, HDA15 and MAC3A/MAC3B reduce the histone acetylation level of the genomic regions near ABA-responsive IRs. Our studies uncovered the role of histone deacetylation in ABA-mediated splicing regulation and identified that HDA15-MAC3A/MAC3B acts as an important regulation module to mediate splicing of introns in ABA responses. One Sentence SummaryHDA15 and MAC3A/MAC3B coregulate intron retention and reduce the histone acetylation level of the genomic regions near ABA-responsive retained introns.

plant biology↗