Biology subjects

Hsieh, H.-Y.

Publications and source records attributed to Hsieh, H.-Y..

4 recordsLinked to original sources

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↗

bioRxiv2023

Bioremediation of Atrazine and its Metabolite Using Multiple Enzymes Delivered by a Bacillus thuringiensis Spore Display System

Atrazine (ATR), a widely used herbicide in the United States, has contaminated ground and surface water. The persistence in the environment, the carcinogenic characteristic, and the endocrine disruption activity of ATR raises public health concerns. To provide a clean source of drinking water, it is imperative to remediate ATR and its metabolites without toxic by-products. A green technology, Bacillus thuringiensis spore-based display system, has been developed to express a high density of enzymes on the spore surface. The B. thuringiensis spore can serve as a bioparticle to deliver enzymes to different environments and enhance the stability and shelf-life of enzymes expressed on their surface. A cluster of enzymes, AtzA, AtzB, AtzC, AtzD, AtzE, and AtzF, found in Pseudomonas sp. strain ADP, remediates ATR to CO2 and NH3 in the degradation pathway. AtzA-bearing spores were generated, and they successfully demonstrated the capability of converting ATR to its metabolite, hydroxyatrazine (HA) [Hsieh et al. 2020]. In this study, AtzB, a hydroxyatrazine N-ethylaminohydrolase that hydrolyzes HA to N-isopropylammelide (NiPA), was expressed on the Bacillus spores by fusing atzB to the gene encoding the attachment domain of the BclA spore surface nap layer protein. The results showed that 1 mg AtzB-bearing spores degraded 50% of HA to NiPA in water within 12 hours. The Km and Vmax of AtzB-bearing spores with HA as a substrate were 25.28 {micro}M and 1.26 nmole NiPA h-1 mg-1 spores, respectively. The optimal ratio of 1:2 for AtzA-bearing to AtzB-bearing spores was applied and successfully converted 90% ATR to NiPA in the water after 96 hours of incubation. The surface water with the addition of 34.5 nM (7.5 {micro}g L-1) of ATR was treated with a combination of AtzA-bearing and AtzB-bearing spores in a 96-hour time course study. Over 80% of applied ATR in surface water was degraded and ATR concentration was below the United States Environmental Protection Agency maximum contaminant level, 13.8 nM (3 {micro}g L-1) within 24 hours. At the end of 96 hours. ATR in surface water was completely converted to NiPA. We have successfully demonstrated the application of multienzyme bioremediation of ATR using the Bacillus spore-based display system in the surface water in the laboratory.

synthetic biology↗

bioRxiv2021

The U1 snRNP component RBP45d regulates temperature-responsive flowering in Arabidopsis thaliana

Pre-mRNA splicing is a crucial step of gene expression whereby the spliceosome produces constitutively and alternatively spliced transcripts that not only diversify the transcriptome but also play essential functions during plant development and responses to environmental changes. Numerous evidences indicate that regulation at the pre-mRNA splicing step is important for flowering time control, however the components and detailed mechanism underlying this process remain largely unknown. Here, we identified a previously unknown splicing factor in Arabidopsis thaliana, RNA BINDING PROTEIN 45d (RBP45d), a member of the RBP45/47 family. Using sequence comparison and biochemical analysis, we determined that RBP45d is a component of the U1 small nuclear ribonucleoprotein (U1 snRNP) with functions distinct from other family members. RBP45d associates with the U1 snRNP by interacting with pre-mRNA-processing factor 39a (PRP39a) and directly regulates alternative splicing (AS) for a specific set of genes. Plants with loss of RBP45d function exhibit defects in temperature-induced flowering potentially due to the mis-regulation of temperature-sensitive AS by RBP45d and PRP39a of the key flowering gene FLOWERING LOCUS M. Taken together, we report that RBP45d is a novel U1 snRNP component in plants that functions together with PRP39a in temperature-mediated flowering.

plant biology↗

bioRxiv2021

A new method to identify global targets of RNA-binding proteins in plants

BackgroundRNA-binding proteins (RBPs) play crucial roles in various aspects of post-transcriptional gene expression; their functions can vary between tissues, cell types, developmental stages, and environmental conditions. Identifying RBP target RNAs and investigating whether they are differentially bound by RBPs in different cell types, stages, or conditions could shed light on RBP functions. Although several strategies have been designed to identify RBP targets, they involve complicated biochemical steps and require large quantities of material, and only a few studies using these techniques have been performed in plants. The TRIBE (targets of RNA binding proteins identified by editing) method was recently developed to identify RBP targets using a RBP coupled to the catalytic domain of a Drosophila RNA editing enzyme and expressing this fusion protein in vivo. The resulting novel editing events can be identified by sequencing. This technique uses little material and does not require complex biochemical steps, however it is not yet adapted for use in plants. ResultsWe successfully applied an optimized genome-wide TRIBE method in plants. We selected the splicing regulator polypyrimidine tract-binding protein (PTB) as a model protein for testing the TRIBE system in the moss Physcomitrium patens. We demonstrated that 13.81% of protein-coding gene transcripts in P. patens are targets of PTB. Most potential PTB binding sites are located in coding sequences and 3 untranslated regions, suggesting that PTB performs multiple functions besides pre-mRNA splicing in this moss. In addition, TRIBE showed reproducible results compared to other methods. ConclusionsWe have developed an alternative method based on the TRIBE system to identify RBP targets in plants globally, and we provide guidance here for its application in plants.

plant biology↗