Online Registration (Deadline: January 29, 2020)


Topic: Making a difference: stomatal biology in a changing world

Speaker: Dr. Dominique Bergmann

Date: 15:00 Wednesday, December 18

Venue: Auditorium A134, Agricultural Technology Building

Wu et al., 2019, Scientific Reports

Lignins are common phenolic compounds present in plant cell walls. In pulp and paper industry, it is necessary to remove lignins from cellulose fibers due to their deep color. However, the chemical degradation of lignins heavily relies on chlorides that have severe impacts on our environments. Laccases are copper-containing oxidases that can oxidize and degrade phenolic compounds, providing an eco-friendly alternative for lignin degradation. Our recent research (Wu et al*. 2019) discovered that the activity of fungal laccases were 2 – 3 fold enhanced in the presence of certain organic solvents (e.g. 30% acetone), together with increase in their protein stabilities. The enhancement is reversible and did not affect the crystal structure of laccase protein. The research will be beneficial in improving the lignin processing efficiency of laccases and decrease the cost of its use in industry.

* Meng-Hsuan Wu and Meng-Chun Lin contributed equally


Kao et al., 2019, Biotechnology for Biofuels

To produce second-generation biofuels and other valuables chemical compounds, enzymatic catalysis is required to convert cellulose from lignocellulosic biomass into fermentable sugars. b-glucosidases finalize the process by hydrolyzing cellobiose into glucose, so the efficiency of cellulose hydrolysis is largely dependent on the quantity and quality of these enzymes used during saccharification. Dr. Tuan-Hua David Ho and his research team have discovered the fungal b-glucosidase D2-BGL from a Taiwanese indigenous fungus Chaetomella raphigera. (Kao et al. 2019 Biotechnology for Biofuels). Recombinant D2-BGL expressed in yeast displayed significantly higher substrate affinity than the commercial b-glucosidase Novozyme 188 (N188). Compared to N188, use of D2-BGL halved the time necessary to produce maximal levels of ethanol by a semi-simultaneous saccharification and fermentation process.  When combined with Trichoderma reesei cellulases, it hydrolyzed acid-pretreated lignocellulosic biomasses more efficiently than the commercial cellulase mixture CTec3. Crystal structure analysis revealed that D2-BGL belongs to glycoside hydrolase (GH) family 3. The F256 substrate-binding residue in D2-BGL is located in a shorter loop surrounding the active site pocket relative to that of Aspergillus b-glucosidases, and this short loop is responsible for its high substrate affinity toward cellobiose.



Bhaskara et al., 2019

Protein phosphorylation is one of the most widespread post-translational modifications which affect protein function.  Phosphorylation is important in many types of signaling in part because it is dynamic.  Phosphorylation by protein kinases can be readily reversed by protein phosphatases.  Improved analytical techniques have led to greater appreciation of the vastness of the plant phosphoproteome.  In the model plant Arabidopsis, there may be as many as 35,000 protein phosphorylation sites on more than 6000 phosphoproteins.  In a recent review (Bhaskara et al., 2019) considered the question of why plants have more then 1000 kinases for protein phosphorylation yet, the flip side of protein dephosphorylation is managed by only about 150 phosphatases.  Of these protein phosphatases, by far the largest group is the type 2C protein phosphatases (PP2Cs), which have greatly expanded numbers in plants compared to other eukaryotes.  We also described new data on function of individual PP2Cs such as the EGR PP2Cs, which the Verslues laboratory and others have found to be new players in abiotic stress signaling.


Chong et al., 2019 PNAS

The ability of plants to acclimate and maintain productivity under changing environmental conditions is important because of climate change and increasing demands on agriculture. Plant acclimation to abiotic stresses such as drought involves multiple layers of gene regulation and post-translational protein modifications. Pre-mRNA splicing, particularly intron retention (IR), is altered by stress yet little is known about how stress signaling impinges upon the splicing machinery to cause such changes. In previous research, the Verslues laboratory noted that the protein phosphatase Highly ABA-Induced 1 (HAI1) has especially prominent effects on drought phenotypes such as growth and proline accumulation.  A screen for HAI1 interacting proteins identified a protein of unknown function, HAI1 Interacting Protein 1 (HIN1) (Chong et al., 2019 PNAS).  HIN1 is a new type of plant-specific RNA-binding protein that affects splicing efficiency of IR-prone introns.  HIN1 is involved in enhanced splicing efficiency of IR-prone introns that occurs during drought acclimation and interacts with several splicing regulators.  HIN1 can be dephosphorylated by HAI1 and may also recruit HAI1 to dephosphorylate other splicing regulators.  This later hypothesis is consistent with our previous phosphoproteomics analysis (Wong et al., 2019 PNAS) which identified splicing factors and RNA binding proteins as putative targets of HAI1-regulated dephosphorylation. Together these data show that HAI1-HIN1 regulation is a new mechanism connecting stress signaling to pre-mRNA splicing.


Nakamura et. al., 2019, iScience

Arabidopsis FT is a pivotal component of florigen, a long-range mobile flowering signal. A research team led by Dr. Nakamura previously discovered that FT interacts with diurnally oscillating phosphatidylcholine molecular species to regulate the flowering (Nakamura et al, 2014 Nat Commun doi:10.1038/ncomms4553). However, the structural basis for the FT-lipid interaction in flowering time control remained elusive. Here, an international and interdisciplinary collaboration team led by Dr. Nakamura and Prof. Inaba (Tohoku Univ, Japan) combined their newly obtained high-resolution crystal structure of FT and computational molecular simulation to identify a lipid-binding site in FT that is required for FT-mediated flowering time control in vivo. The result opens a new avenue in investigating the molecular mechanism of flowering time control by lipids, which may contribute to development of an innovative agricultural technology.


Lipids are the basic components of the endomembrane system. Lipid synthesizing enzymes catalyze lipid synthesis mostly at the endoplasmic reticulum (ER), and the forming lipids are sorted through a complicated network to reach their final destination in the cell. It is conceivable that lipid synthesis is precisely controlled to cope with cell physiology. However, most of the mechanisms remain unclear. Our recent findings reveal that the human congenital generalized lipodystrophy (CGL) protein seipin regulates sphingolipid production at the contact site between ER and lipid droplets (LDs). Sphingolipids, essential components of the plasma membrane, are controlled by the cell to maintain homeostasis. Seipin interacts with two key enzymes of the sphingolipid synthesis pathways to inhibit their activities. When the cellular sphingolipid level is reduced, seipin dissociates from the two key enzymes, enabling the sphingolipid precursor termed ceramide being produced at the ER-LD contacts. The novel mechanism is published in the Journal of Cell Biology. Given that seipin is a disease-linked protein, further analysis is necessary to know whether the mechanism is involved in the etiology of the human CGL disease.

Matzke, A.J.M., Lin, W.D., and Matzke, M., 2019, Front. Plant Sci.

We have developed tools and performed pilot experiments to test the hypothesis that an intracellular ion-based signaling pathway, provoked by an extracellular stimulus acting at the cell surface, can influence interphase chromosome dynamics and chromatin-bound proteins in the nucleus. The experimental system employs chromosome-specific fluorescent tags and the genome-encoded fluorescent pH sensor SEpHluorinA227D, which has been targeted to various intracellular membranes and soluble compartments in root cells of Arabidopsis thaliana. We are using this system and three-dimensional live cell imaging to visualize whether fluorescent-tagged interphase chromosome sites undergo changes in constrained motion concurrently with reductions in membrane-associated pH elicited by extracellular ATP, which is known to trigger a cascade of events in plant cells including changes in calcium ion concentrations, pH, and membrane potential. To examine possible effects of the proposed ion-based signaling pathway directly at the chromatin level, we generated a pH-sensitive fluorescent DNA binding protein that allows pH changes to be monitored at specific genomic sites. Results obtained using these tools support the existence of a rapid, ion-based signaling pathway that initiates at the cell surface and reaches the nucleus to induce alterations in interphase chromatin movement and the surrounding pH of chromatin-bound proteins. Such a pathway could conceivably act under natural circumstances to allow external stimuli to swiftly influence gene expression by affecting interphase chromosome mobility and the structures and/or activities of chromatin-associated proteins.