Noriyuki Konishi: The Plant Cell First Author

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Noriyuki Konishi, first author of “Polar localization of a rice silicon transporter requires isoleucine at both C- and N-termini as well as positively charged residues”

Current Position:

Assistant professor, Okayama University, Japan

Education:

B.S. (2008-2012) and Ph.D. (2012-2017) in Graduate School of Agricultural Science, Tohoku University, Japan

Brief bio:

Before starting my academic career, I devoted most of my time to horses because I was a member of the equestrian team at Tohoku University. Honestly, I was not motivated to study science at that time, but after I joined Tomoyuki Yamaya’s lab of plant nutrition, I gradually became interest in studying plant science, similar to being fascinated with my lovely horses. During my Ph.D. course, I investigated the mechanisms of ammonium assimilation in Arabidopsis. After that, I joined Jian Feng Ma’s lab as a post-doctoral researcher in 2017 and started working on the mechanism underlying the polar localization of mineral transporters in rice, especially silicon transporter OsLsi1. In the present study, we identified critical residues required for the polar localization of OsLsi1 and revealed the importance of polar localization in efficient silicon uptake.  Since the mechanisms for the polar localization of most mineral transporters are still unclear, especially in rice, I will continue to work on this project to gain the whole picture of polar localization mechanisms.

Alexander J. Cummins: Plant Physiology First Author

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Alexander J. Cummins, first author of “A cryptic natural variant allele of BYPASS2 suppresses the bypass1 mutant phenotype”

Current Position: Ph.D. Student in the School of Biological Sciences at the University of Utah

Education: B.S. in Biology from California State University San Bernardino

Non-scientific interests: Reading, cooking, spending time with family

Brief Bio: During my undergraduate degree, I became very interested in understanding how plants respond and adapt to changes in their local environment. For this reason, I joined the lab of Dr. Leslie Sieburth at the University of Utah. Our research focuses on a novel signaling pathway discovered in the Arabidopsis mutant bypass1.  This pathway uses a metabolite-derived signaling molecule which we call dalekin.  Dalekin is synthesized in roots, is mobile in plants and it activates processes in both roots and shoots.  We use a combination of genetics, molecular biology, multi-omics, and physiological approaches to understand dalekin’s biosynthetic pathway and the signal transduction pathway used to activate down-stream responses.  A key future goal is to understand the roles dalekin plays in plants.   

Katie M. Murphy: Plant Physiology First Author

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Katie M. Murphy, first author of “A dolabralexin-deficient mutant provides insight into specialized diterpenoid metabolism in maize”

Current Position: Director of Phenotyping & Principal Investigator, Donald Danforth Plant Science Center

Education: PhD in Plant Biology from UC Davis, BS in Chemistry from Stanford University

Non-scientific Interests: Quilting and following Formula 1 racing

Brief bio: 

As the Danforth Center Director of Phenotyping, I manage our controlled environment and field phenotyping facility, where we run large, high-throughput phenotyping experiments to help internal and external research groups answer questions about plant phenotypes. In addition to running our facility, my research team applies image-based phenotyping to understand how maize responds to heat stress, which builds upon my graduate research on maize diterpenoids in Dr. Philipp Zerbe’s lab and my postdoctoral work in Dr. Malia Gehan and Dr. Doug Allen’s labs. Science communication is a passion of mine, and I share our work through my TikTok account @Real_Time_Science.

Fabin Yang: The Plant Cell First Author

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Fabin Yang, co-first author of “Inhibition of SIZ1-mediated SUMOylation of HOOKLESS1 promotes light-induced apical hook opening in Arabidopsis”

Current Position: Ph.D. candidate, Sichuan University

Education: Master’s degree, Qufu Normal University

Non-scientific Interests: Playing basketball and watching movies

Brief bio: I began my doctoral study in Prof. Dawei Zhang’s research group in 2020, mainly study the molecular mechanism of how SUMOylation regulates plant development. Our study found that the SUMO E3 Ligase SAP AND MIZ1 DOMAIN- CONTAINING LIGASE1(SIZ1) can positively regulate the apical hook development. Moreover, SIZ1 can interact with the HLS1 (HOOKLESS1), a central regulator of apical hook development. SIZ1 mediates the SUMOylation of HLS1, which is crucial for the apical hook development. Upon exposure to the light, HY5 suppresses SIZ1 transcription, decreasing HLS1 SUMOylation and thus initiating the apical hook quickly opening. Our study not only finds a post-translational modification of HLS1, but also reveals a rapid regulatory mechanism of apical hook opening via a SIZ1-mediated HLS1 SUMOylation.

姓名：杨发斌

目前职位：四川大学生命科学学院，在读博士生

教育背景：曲阜师范大学，硕士学位

兴趣爱好：打篮球，看电影

个人简介：我于2020年开始在张大伟教授的课题组攻读博士学位，主要研究类泛素修饰SUMO化调控植物发育的分子机制。我们的研究发现SUMO E3连接酶SAP AND MIZ1 DOMAIN- CONTAINING LIGASE1（SIZ1）可以正向调控顶端弯钩的生长发育，并且SIZ1可与顶端弯钩发育的核心调控因子HLS1（HOOKLESS1）相互作用。SIZ1可以介导HLS1的SUMO化，这对于顶端弯钩的发育至关重要。光照条件下，HY5抑制SIZ1的转录，减弱HLS1的SUMO化修饰，减少寡聚体的形成从而导致顶端弯钩的快速展开。我们的研究不仅发现了HLS1的翻译后修饰，同时也揭示了植物通过SIZ1介导的HLS1的SUMO化修饰调控顶端弯钩发育的分子机制。

Jiawei Xiong: The Plant Cell First Author

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Jiawei Xiong, co-first author of “Inhibition of SIZ1-mediated SUMOylation of HOOKLESS1 promotes light-induced apical hook opening in Arabidopsis“

Current Position: Ph.D. candidate, Sichuan University

Education: Bachelor’s degree, Sichuan Agricultural University

Non-scientific Interests: Reading and watching movies

Brief bio: After my graduation from Sichuan Agricultural University in 2017, I began my doctoral study in Prof. Dawei Zhang’s research group, focused on the molecular mechanism of photomorphogenesis in plants. In this study, we demonstrate that the SUMO E3 ligase SIZ1 interacts with HLS1 and mediates HLS1 SUMOylation. Mutating SUMO attachment sites of HLS1 results in impaired function of HLS1, indicating that HLS1 SUMOylation is essential for its function. SUMOylated HLS1 is more likely to assemble into oligomers, which are the active form of HLS1. During the dark-to-light transition, light induces the quick opening of the apical hook, concomitantly with a drop in SIZ1 transcript levels, resulting in lower HLS1 SUMOylation. Furthermore, we discover that HY5 directly binds to the SIZ1 promoter and suppresses its transcription. HY5-initiated rapid apical hook opening partially depends on the HY5-SIZ1 transcriptional inhibition. Our study identifies a function for SIZ1 in apical hook development, providing a dynamic regulatory mechanism linking the post-translational modification of HLS1 during apical hook formation and light-induced apical hook opening.

姓名：熊佳威

目前职位：四川大学生命科学学院，在读博士生

教育背景：四川农业大学，学士学位

兴趣爱好：阅读，看电影

个人简介：在2017年从四川农业大学本科毕业后，我在张大伟教授的课题组开始攻读博士学位，主要研究植物光形态建成的分子机制。在本研究中，我们证明了SUMO E3连接酶SIZ1与HLS1相互作用并介导HLS1的SUMO化。突变HLS1的SUMO附着位点会导致HLS1的功能受损，这表明HLS1的SUMO化对其功能至关重要。SUMO化的HLS1更容易组装成活性的寡聚物形式。在从黑暗到光照的转换过程中，光诱导顶端钩的快速打开，同时伴随着SIZ1转录水平的下降，导致HLS1的SUMO化水平降低。此外，我们还发现HY5直接结合到SIZ1的启动子并抑制其转录。HY5介导的顶端钩快速打开是部分依赖于HY5-SIZ1的转录抑制。我们的研究揭示了SIZ1介导的HLS1的SUMO化在顶端钩发育过程中的重要作用，提出了一个将HLS1在顶端钩形成过程中的翻译后修饰与光诱导的顶端钩打开联系起来的动态调节机制。

Kai-Chun Peng: Plant Physiology First Author

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Kai-Chun Peng, first author of “FAR-RED INSENSITIVE 219 and phytochrome B co-repress shade avoidance via modulating nuclear speckle formation”

Current Position:

Ph.D. candidate, Institute of Plant Biology, College of Life Science, Nation Taiwan University, Taipei, Taiwan

Education:

Ph.D. candidate in Plant Biology, National Taiwan University; B.Sc. in Biological Science and Technology, National Chiao Tung University

Non-scientific Interests: Badminton, Photography, and Hiking

Brief biography:

I joined Prof. Hsu-Liang Hsieh’s lab to pursue a Ph.D. degree in plant science at National Taiwan University in 2014. My research is specifically focused on the regulation between the jasmonic and light signaling pathways in Arabidopsis. Then I got interested in the growth-defense tradeoffs under a shading environment, which is a dilemma in most plant species. We characterized a novel regulation that FIN219/JAR1 and phyB co-repress the shade avoidance response via modulating the phyB-mediated nuclear speckle formation, and it depends on the abundance of jasmonic acid. In the future, we are dedicated to uncovering the detailed mechanism of JA-triggered nuclear speckle formation, which remains largely unknown.

How EXECUTER1 executes chloroplast-to-nucleus signaling in response to singlet oxygen

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Li et al. identify the signaling pathway regulated by the chloroplast-localized protein EXECUTER1 in response to singlet oxygen.

 Background: In response to developmental and environmental cues such as changing light intensity, plastids/chloroplasts produce and emit signals such as singlet oxygen, 1O2. These signals broadly affect the expression of nuclear genes, thereby altering chloroplast function to help the plant develop and acclimate to the changing environment. This signaling process is termed retrograde signaling. The chloroplast-localized protein EXECUTER1 (EX1) is required for 1O2-triggered retrograde signaling.

Question: What are the biochemical properties of EX1 and how is 1O2-mediated retrograde signaling transduced from plastids to the nucleus?

 

Findings: Using a forward genetic screen in Arabidopsis thaliana, we identified GENOMES UNCOUPLED4 (GUN4) and GUN5 as two suppressors of a pif1 pif3 double mutant, which lacks the function of PHYTOCHROME-INTERACTING FACTOR1 (PIF1) and PIF3. GUN4 and GUN5 interacted with EX1 and its homolog EX2 in plastids, and 1O2 prevented this interaction. The gun4, gun5, ex1, and ex2 mutants showed increased tolerance of high light, whereas seedlings overexpressing GUN4 or EX1 were sensitive to photobleaching. Upon induction by 1O2, EX1 transiently accumulated and translocated from plastids to the nucleus and the nuclear targeting of EX1 was required for its function. In the nucleus, EX1 interacted with the transcription factors WRKY18 and WRKY40 and functioned as a transcriptional co-activator to promote the expression of 1O2-responsive genes. We propose a working model in which EX1 directly mediates retrograde 1O2 signaling from plastids to the nucleus.

Next steps: We are interested in how EX1 is spatially regulated in the retrograde 1O2 signaling pathway.

Reference:

Yuhong Li, Hanhong Liu, Tingting Ma, Jialong Li, Jiarui Yuan, Yong-Chao Xu, Ran Sun, Xinyu Zhang, Yanjun Jing, Ya-Long Guo, Rongcheng Lin (2023). Arabidopsis EXECUTER1 interacts with WRKY transcription factors to mediate plastid-to-nucleus singlet oxygen signaling. https://doi.org/10.1093/plcell/koac330

Truncated organellar C-to-U RNA editing enzyme requires active site complementation

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Toma-Fukai and Sawada et al. provide insight into the activation mechanism of the DYW1-like deaminase.

By Sachiko Toma-Fukai1,2 Mizuki Takenaka3 and Toshiyuki Shimizu1

1 Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

2 Present address: Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan

3 Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan.

Background: In terrestrial plants, C-to-U RNA editing occurs in mitochondrial and chloroplast genes. More than one hundred pentatricopeptide repeat (PPR) proteins have been identified as specificity factors for RNA editing. The DYW deaminase domain in PPR proteins serves as an enzyme for C-to-U conversion. More than half of the PPR-type RNA editing factors, however, lack the DYW cytidine deaminase domain. Genetic analyses have suggested that their enzymatic activity arises by association with a family of DYW1-like proteins that contain an N-terminally truncated DYW domain. Nevertheless, the mechanism underlying the activation of the truncated DYW deaminase remains largely unknown.

Question: What is the structural mechanism underlying activation of the DYW1-like deaminase?

Findings: We determined the crystal structure of the N-terminally truncated DYW domain from Arabidopsis thaliana DYW1. DYW1 forms a cytidine deaminase fold and a C-terminal DYW motif harboring two zinc ions but lacks two structurally conserved β-strands corresponding to the PG box. The recruitment of the PG box and its flanking region from CRR4 likely enables the pocket to accommodate the substrate, conferring catalytic activity to DYW1. In vivo RNA editing assays corroborate that the presence of a PG box in the vicinity of DYW1 is required for its deaminase activity.

Next steps: The results described here will provide valuable information for developing the DYW domain as a controllable genetic manipulation tool. Further structural studies of DYW1 in complex with its partner proteins are required to shed light on its editing mechanism.

Sachiko Toma-Fukai, Yuto Sawada, Ayako Maeda, Hikaru Shimizu, Toshiharu Shikanai, Mizuki Takenaka　and Toshiyuki Shimizu. (2023). Structural insight into the activation of an Arabidopsis organellar C-to-U RNA editing enzyme by active site complementation https://doi.org/10.1093/plcell/koac318

Plastid Nucleoside Kinase 1 (PNK1) phosphorylates inosine to inosine monophosphate, involving in the feedback control of purine de novo synthesis in Arabidopsis

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Chen et al. identify a nucleoside kinase that is highly conserved in plants and green algae.

By Xiaoguang Chen and Claus-Peter Witte. Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany.

Background: Nucleotides are the building blocks for DNA and RNA and are energy carriers (ATP) as well as precursors for many other key cellular molecules. Nucleotide metabolism in plants is conceptually divided into: (i) biosynthesis producing nucleotides from scratch from simple molecules, (ii) degradation leading to the complete decomposition of nucleotides, and (iii) salvage reactions that recycle nucleotide building blocks into nucleotides. Nucleoside kinases act in salvage by adding a phosphate group to nucleosides, which are precursors of nucleotides that lack a phosphate group.

Question: Nucleoside kinases for several nucleosides have been identified in many organisms, but kinases for certain important nucleosides, in particular inosine and guanosine, remain to be identified, except for a few examples from bacteria. It was long suspected that plants have such kinase(s) and we wanted to find the respective gene(s) and understand the function of the corresponding protein(s).

Findings: In this study, we identified PLASTID NUCLEOSIDE KINASE 1 (PNK1), an enzyme highly conserved in plants and green algae. We demonstrate that PNK1 from Arabidopsis thaliana is located in plastids and can phosphorylate inosine and uridine (but not guanosine) to produce the respective nucleotides inosine monophosphate (IMP) and uridine monophosphate (UMP). Mutation of PNK1 leads to less inosine salvage reducing the plant’s IMP content and increasing nucleotide degradation. Under certain conditions, the UMP content is also altered. We suggest that PNK1 acts in nucleoside salvage and contributes to the control of flux through nucleotide biosynthesis.

Next steps: It will be interesting to investigate how PNK1 is integrated into a regulatory network that ensures an adequate rate of nucleotide biosynthesis for the cellular needs. Which other components are part of this network and how does it operate?

Xiaoguang Chen, Sang-Hoon Kim, Sangkee Rhee, Claus-Peter Witte. (2023). A plastid nucleoside kinase is involved in inosine salvage and control of purine nucleotide biosynthesis https://doi.org/10.1093/plcell/koac320