Liu et al., 2018, The Plant Journal

Phosphatidylcholine (PtdCho) is the conserved membrane lipid component among eukaryotic cells yet playing multiple biological roles beyond a constituent of cellular membranes. In plants, the phospho-base N-methyltransferases (PMTs) catalyze the biosynthesis of phosphocholine (PCho), a prerequisite for PtdCho biosynthesis. However, it remains elusive whether specific PMT isoform is involved in PtdCho biosynthesis in Arabidopsis. A research project led by Dr. Yuki Nakamura revealed that two isoforms of PMT, PMT1 and PMT3, redundantly play an essential role in PCho biosynthesis in Arabidopsis. Double mutation of PMT1 and PMT3 contained trace amount of PCho and affected PtdCho biosynthesis in vivo, showing severe growth defect due to defective leaf vein patterning. This study highlights the importance of PMT1 and PMT3 in PCho biosynthesis, which are required for PtdCho biosynthesis, and possible roles of these metabolites in vascular development in Arabidopsis.

Hsieh et al., 2018, Scientific Reports

Fig. 1 Phenotypes of 10-day-old rice seedlings grown in hydroponic solutions with (+N) or without (-N) nitrogen. 

 

Nitrogen (N) deficiency is one of the most common problems in rice. The symptoms of N deficiency are well documented (Fig. 1), but the underlying molecular mechanisms are largely unknown in rice. Dr. Ming-Hsiun Hsieh’s laboratory reported that levels of glutamine rapidly decreased within 15 min of -N treatment, indicating that part of the N-deficient signals could be mediated by glutamine (Hsieh et al., 2018, Sci Rep 8: 12207). Transcriptome analysis revealed that genes involved in metabolism, plant hormone signal transduction (e.g. abscisic acid, auxin, and jasmonate), transporter activity, and oxidative stress responses were rapidly regulated by -N. Contributors of this work include: Ping-Han Hsieh, Chia-Cheng Kan, Hsin-Yu Wu and Hsiu-Chun Yang. (http://www.nature.com/articles/s41598-018-30632-1)

He et al. Plant Physiology 2018

Successful pollen tube elongation is critical for double fertilization. Understanding the biological functions of pollen tube genes will provide new insights into the regulatory machinery underlying this crucial process. He et al. from Dr. Guang-Yuh Jauh’s laboratory identified two Arabidopsis Small Auxin Up RNA genes, SAUR62 and SAUR75, with expression upregulated by pollination according to previous translatomic study  (Lin et al. Plant Cell 2014). Both SAUR62 and SAUR75 mainly localized in pollen tube nuclei, and siliques of homozygous saur62 (saur62/-), saur75 (saur75/-), and the SAUR62/75 RNAi knockdown line had many aborted seeds. Pollen viability of these mutants and RNAi lines was normal, but in vitro and in vivo pollen tube growth was defective, with branching phenotypes. Immunoprecipitation with transgenic SAUR62/75-GFP flowers revealed ribosomal protein RPL12 family members as their potential partners, and their individual interactions were further confirmed by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation assay (BiFC). Polysome profiling showed reduced 80S ribosome abundance in homozygous saur62, saur75, rpl12c and SAUR62/75 RNAi flowers, which suggests roles for SAUR62/75 in ribosome assembly. To clarify the roles in translation, total proteins of wild-type (WT) and RNAi flowers were analyzed by iTRAQ, which revealed significantly reduced expression of factors participating in pollen tube wall biogenesis and F-actin dynamics, critical for the elastic properties of tube elongation. Indeed, RNAi pollen tubes showed dislocalization of de-esterified and esterified pectins and F-actin organization. Here, we demonstrate the biological roles of SAUR62/75 and their partners, RPL12 family members, as critical in ribosome assembly for efficient pollen tube elongation and the following fertilization (He et al. Plant Physiology 2018).

Huang et al., 2018, Plant Physiology

Photoperiodic floral induction is controlled by the leaf-derived and antagonistic mobile signals florigen and antiflorigen. Florigen and antiflorigen are encoded by a pair of homologues belong to PEBP gene family. In many plants, protein movement of PEBP genes is an evolutionarily conserved mechanism; however, mRNA movement of PEBP genes remains controversial. A recent publication from Dr. Tien-Shin Yu’s lab provided evidences to show that multiple members in FT-, TFL1- and MFT-like clades of tobacco and tomato PEBP genes are mobile mRNAs, which raises an intriguing possibility that the mRNA mobility may be an early evolutionary event that occurred before the divergence of FT/TFL1-like clades from MFT-like clades (Huang et al., Plant Physiol., 2018).

Singh et al., 2018, Scientific Reports

Fig. 1 A working model of ACR11 function in modulating ROS production and SA-associated defense responses. 

Dr. Ming-Hsiun Hsieh’s laboratory reported that ACR11 may function as a putative glutamine sensor in Arabidopsis (Singh et al., 2018, Sci Rep 8: 11851). The ACR11 protein contains two ACT domain repeats. Dr. Hsieh’s group characterized two independent acr11 mutants in Arabidopsis. The acr11 mutants have a lesion-mimic phenotype accompanied by increased levels of reactive oxygen species (ROS) and salicylic acid (SA)-associated defense responses. Based on their study and the literature, Dr. Hsieh’s group proposed that ACR11 may play an important role in the interconnections of glutamine homeostasis, GS/Fd-GOGAT cycle, redox balance, ROS accumulation, and SA-associated defense responses in Arabidopsis (Fig. 1). Contributors of this work include: Shashi Kant Singh, Tzu-Ying Sung, Tsui-Yun Chung, Shao-Yu Lin, Sang-Chu Lin, Jo-Chien Liao and Wei-Yu Hsieh.

Hsu et al., 2018, Epigenomes

Figure: Methylome and transcriptome analysis during rice regeneration.

We collected embryo, callus (induction, subculture), failed and successful regenerants from japonica and indica rice, and performs whole genome bisulfite sequencing and RNA-seq. From the analysis we see significant cluster in methylome and transcriptome based on cultivars, suggesting DNA methylation might be a factor of impacting the efficiency of rice regeneration.

Oryza sativa indica (cv. IR64) and Oryza sativa japonica (cv. TNG67) vary in their regeneration efficiency. Such variation may occur in response to cultural environments that induce somaclonal variation. Somaclonal variations may arise from epigenetic factors, such as DNA methylation. We hypothesized that somaclonal variation may be associated with the differential regeneration efficiency between IR64 and TNG67 through changes in DNA methylation. We generated the stage-associated methylome and transcriptome profiles of the embryo, induced calli, sub-cultured calli, and regenerated calli (including both successful and failed regeneration) of IR64 and TNG67. We found that stage-associated changes are evident by the increase in the cytosine methylation of all contexts upon induction and decline upon regeneration. These changes in the methylome are largely random, but a few regions are consistently targeted at the later stages of culture. The expression profiles showed a dominant tissue-specific difference between the embryo and the calli. A prominent cultivar-associated divide in the global methylation pattern was observed, and a subset of cultivar-associated differentially methylated regions also showed stage-associated changes, implying a close association between differential methylation and the regeneration programs of these two rice cultivars. Based on these findings, we speculate that the differential epigenetic regulation of stress response and developmental pathways may be coupled with genetic differences, ultimately leading to differential regeneration efficiency. The present study elucidates the impact of tissue culture on callus formation and delineates the impact of stage and cultivar to determine the dynamics of the methylome and transcriptome in culture.

2019 Admission of the NCU-AS Graduate Program (Master) 

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