Wenjiao Zou: Plant Physiology First Author

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Wenjiao Zou, first author of “Lipid transport protein ORP2A promotes glucose signaling by facilitating RGS1 degradation”

Current Position: Lecturer, Institute of Pharmacy, Shandong University of Traditional Chinese Medicine

Education: 2008.09-2012.07 College of Life Sciences, Ludong University, Undergraduate, 2012.09-2015.07 College of Life Sciences, Shandong Agricultural University, Postgraduate, 2015.09-2020.12 College of Life Sciences, Shandong Agricultural University, Doctoral candidate.

Non-scientific Interests: Enjoying music, watching movies

Brief bio: Since my postgraduate study in 2015, my main research direction is the plant molecular developmental biology, mainly exploring the mechanism of Arabidopsis lipid transport protein ORP2A regulating organ morphological development and sugar signaling. Now, I am mainly engaged in the growth and development of medicinal plants related research.

姓名：邹文娇

现状：山东中医药大学 药物研究院 讲师

教育程度：2008.09-2012.07 鲁东大学生命科学学院 大学本科，2012.09-2015.07 山东农业大学生命科学学院 硕士研究生，2015.09-2020.12山东农业大学生命科学学院 博士研究生。

兴趣爱好：听音乐、看电影

自我介绍：自2015年攻读研究生期间主要研究方向为植物分子发育生物学，主要探索了拟南芥脂类运输蛋白ORP2A调控器官形态发育和糖信号的作用机理。现主要从事药用植物生长发育相关研究。

Yuxin Shen: Plant Physiology First Author

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Yuxin Shen, first author of “Complexity and regulation of age-dependent alternative splicing in Brachypodium distachyon”

Current position: Ph.D student at the College of Agriculture and Biotechnology, Zhejiang University, China

Education: 2020, B.Sc. from the College of Agriculture and Biotechnology, Zhejiang University, China

Non-scientific interests: Travelling and walking.

Brief bio: I started my study in agronomy at the College of Agriculture and Biotechnology at Zhejiang University and completed my bachelor’s degree with the help of Prof. Liang Wu. Afterwards, I continue my study on genetics and crop breeding in the lab of Prof. Wu, and my research is mainly focused on the regulatory mechanism of coding and non-coding gene expressions in plants during growth phase transition and responses to heavy metal stresses at genomic and transcriptomic levels.

 

第一作者：沈雨欣

目前职位：浙江大学农业与生物技术学院作物所，博士在读

教育经历：2020年，浙江大学，农学学士

兴趣爱好：旅游和散步

个人简历：我本科期间就读于浙江大学农业与生物技术学院农学专业，并在武亮教授的指导下完成农学学士学位本科毕设。之后我继续在武亮教授实验室作物遗传育种领域开展科学研究，主要研究方向是在基因组和转录组层面，利用生物信息学分析手段，探究植物生长发育阶段转变和响应重金属胁迫过程中编码基因和非编码基因表达调控的作用机制。

 

 

Response and rebalance: Jasmonates make citrus peels brighter

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Yue et al. explore how jasmonates regulate carotenoid production in citrus.

 By Pengtao Yue

Background: Beautiful, bright peel colors attract animals to help disperse seeds and are preferred by consumers. In agricultural production, citrus fruit often suffers from uneven coloration and poor development of color in the fruit peel, which limits fruit value. Carotenoids are natural pigments in plants and the red carotenoid β-citraurin is essential for the peel coloration of ‘Newhall’ orange fruit. Although many signaling pathways are linked to the regulation of carotenoid biosynthesis, how β-citraurin biosynthesis is regulated during citrus fruit development and maturation is still poorly understood, which hampers the development of management strategies for improving citrus fruit coloration. Jasmonates regulate carotenoid biosynthesis, but their role in citrus fruit coloration is unknown.

Question: What are the detailed mechanisms by which jasmonates regulate β-citraurin biosynthesis?

Findings: We found that exogenous methyl jasmonate (MeJA) treatment of ‘Newhall’ orange fruit promoted β-citraurin accumulation and fruit peel coloration. The jasmonate signaling master transcription factor CsMYC2 bound promoters of β-citraurin biosynthetic genes and activated their expression and promoted expression of the MAP kinase gene CsMPK6. In turn, CsMPK6 interacted with CsMYC2 to decrease the promoter binding activity of CsMYC2 to its target promoters. CsMPK6 also phosphorylated CsMYC2 to accelerate its degradation and thus, attenuated the jasmonate response for citrus to prevent the fruit from overreacting to jasmonates.

Next steps: An important task for next step is to explore whether other signaling pathways interact with jasmonates to co-regulate β-citraurin biosynthesis. With that work, we will investigate whether CsMYC2 serves as a mediator to bridge jasmonate signaling with other signaling pathways in regulating citrus coloration.

Reference:

Pengtao Yue, Zhenghua Jiang, Quan Sun, Ranran Wei, Yingzi Yin, Zongzhou Xie, Robert M. Larkin, Junli Ye, Lijun Chai, Xiuxin Deng. (2023). Jasmonate activates a CsMPK6-CsMYC2 module that regulates the expression of β-citraurin biosynthetic genes and fruit coloration in orange (Citrus sinensis). https://doi.org/10.1093/plcell/koac363

Catherine Stuart: The Plant Cell First Author

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Catherine Stuart, co-first author of “RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis”

Current Position:

Research Assistant at the University of Texas Health Science Center (full-time) and Baylor College of Medicine (part-time), Houston, TX

Education:

B.S. in Biology and Genetics (Texas A&M University); M.S. in Biological Sciences (University of Delaware)

Non-scientific Interests:

reading, traveling, going to the movies, doing yoga, spending quality time with my husband and cats

Brief bio:

I joined the Green lab at the University of Delaware in 2019 after completing my B.S. in Biology and Genetics at Texas A&M University. I have always had a passion for understanding basic biological processes, so I was excited to study post-transcriptional mechanisms of gene regulation in a well-established model organism. In the Green lab, I investigated the roles of cytosolic endoribonucleases in Arabidopsis, eventually narrowing my focus to DNE1 due to its evolutionary conservation and homology to metazoan MARF1. Even though I was only a graduate student for a short amount of time, I gained many valuable skills and formed relationships that will last a lifetime. After defending my Master’s thesis in 2021, I joined the van Hoof lab at the University of Texas Health Science Center. In the van Hoof lab, I use the power of yeast genetics to study mechanisms of RNA decay in S. cerevisiae. In 2022, I started a second job in the Arey lab at Baylor College of Medicine, where we study regulators of learning and memory in C. elegans. I am grateful for the experiences and mentors that have helped get me to where I am today. I am also grateful to work for two amazing institutions that support my development as a scientist. I don’t know what the future holds for me, but I do know that my love of learning will always guide me down the right path.

Vinay Nagarajan: The Plant Cell First Author

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Vinay Nagarajan, co-first author of “RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis”

Current Position: 

Scientist, Syngenta Crop Protection, LLC, Research Triangle Park, NC 27709

Education: 

Ph.D., Horticulture, Purdue University, West Lafayette, Indiana, USA

M.S., Plant Biology, Southern Illinois University, Carbondale, Illinois, USA

B.S., Seed Science Technology, Osmania University, Hyderabad, India

Non-scientific Interests: 

Reading and watching science fiction, travelling, cooking, and spending time with my family

Brief bio:

My path to become a Plant Biologist was serendipitous. Initially planning to earn a degree in Biology and specializing in microbiology, I enrolled into a B.S. Biology program at a college affiliated to Osmania University, Hyderabad, India. Unfortunately, that year the Biology Department experienced a spate of retirements, which resulted in a staffing crisis for teaching foundational courses. Not satisfied with the teaching quality and in fear of having to start a new program elsewhere, I made a switch mid-semester to an agriculture-based B.S. program. After graduating at the top of my class, I came to the US for an M.S program in Plant Biology at SIU Carbondale, Illinois. I owe my initial training as a Plant Physiologist to (the late) Dr. Stephen Ebbs, in his lab I investigated arsenic transport and speciation in rice, Indian mustard, and hyperaccumulating ferns. I expanded my skills as a molecular biologist during my Ph.D. program in Dr. K.G Raghothama’s lab at Purdue University. There, I characterized transcriptional programs key to plant phosphate signaling responses that led to several well-cited publications.

My interest in “omics” approaches (especially genomics and transcriptomics) and their impact on plant biology brought me to Dr. Pam Green’s lab at the University of Delaware for my postdoctoral work. I am thankful to Dr. Green for my training in NGS approaches and deeper understanding of plant RNA biology. Working with the RNA degradome that provides a genome-wide snapshot of RNA decay intermediates, introduced me to bioinformatics and analysis of large datasets. Using this approach, I helped identify substrates and novel associations of cytoplasmic exoribonuclease AtXRN4, and more recently mRNAs targeted by endoribonuclease AtDNE1.

As an Associate Scientist in the Green lab, I had a major role in the development, writing and execution of the National Science Foundation grant that funded our work identifying substrates of Arabidopsis endoribonucleases. I also took up the opportunity to train and mentor young scientists. Two especially talented students, Catherine Stuart (co-author, M.S) and undergraduate Anna DiBattista (currently Ph.D. student at UNC Chapel Hill) were instrumental in the characterization of AtDNE1.

Currently, I am using my dual expertise in plant molecular biology and bioinformatics to characterize transgenic events in crop plants at Syngenta.

A Mediator–transcription factor module that regulates fruit ripening in tomato

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Deng, Yang, Li, Chang, Sun et al. explore the interaction between EIN3-like transcription factors and subunits of the Mediator complex in tomato fruit ripening.

Background: Fruit ripening relies on the precise spatiotemporal control of RNA polymerase II (Pol II)-dependent transcription of thousands of ripening-related genes, including regulatory genes and structural genes. In tomato, ethylene is a key signal that regulates fruit ripening. As the master regulators of the ethylene signaling pathway, ETHYLENE INSENSITIVE3 (EIN3)/EIN3-LIKE (EIL) transcription factors play a critical role in fruit ripening. In addition to EILs, a plethora of transcription factors essential for ripening have been identified. The mechanisms underlying the communication between key transcription factors and the Pol II general transcriptional machinery remain largely unknown.

Question: Mediator is an evolutionarily conserved multi-subunit complex that links gene-specific transcriptional factors with Pol II transcriptional machinery. It is unclear which subunit is involved in the transcriptional regulation of tomato fruit ripening.

Findings: We found that the Mediator subunit MED25 physically interacts with EILs, thereby orchestrating an ethylene-dependent transcriptional program for the regulation of ripening-induced gene expression. We demonstrated that MED25 forms a transcriptional module with EILs to regulate the expression of ripening-related regulatory as well as structural genes through promoter binding. We also showed that the EIL1–MED25 module orchestrates both positive and negative feedback transcriptional circuits, along with its downstream regulators, to fine-tune ethylene homeostasis during fruit ripening.

Next steps: One interesting direction for future exploration is to elucidate the functional significance and role of the EIL–MED25-dependent hierarchical transcriptional cascade in regulating fruit ripening.

Reference:

Lei Deng, Tianxia Yang, Qian Li, Zeqian Chang, Chuanlong Sun, Hongling Jiang, Xianwen Meng, Tingting Huang, Chang-Bao Li, Silin Zhong, Chuanyou Li (2023) Tomato MED25 regulates fruit ripening by interacting with EIN3-like transcription factors. https://doi.org/10.1093/plcell/koac349

Review: Stress-related biomolecular condensates in plants

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Biomolecular condensates are non-membrane-bound compartments containing proteins and RNAs with key functions in stress responses. In plants, they occur as several types with different properties and components, including stress granules and processing bodies. Protein domains such as prion-like domains and intrinsically-disordered regions provide stickiness and facilitate protein aggregation. Although much of what is known about biomolecular condensates is derived from studies in yeast and animal cells, our understanding of these processes in plants is accelerating rapidly. This review by Solis-Miranda et al. provides an overview of what is known in plants, including findings from proteomic and transcriptomic studies comparing different condensate types. Interestingly, many of the proteins in these structures are kingdom-specific, with only about 15% of plant proteins shared by yeast or animal structures. The review takes a close look at how these condensates contribute to stress resistance, and the potential to harness them for crop protection. Note: this topic is featured and two of the review authors are speaking at the ASPB Plant Biology conference in August 2023 https://plantbiology.aspb.org/plenaries/. Early registration ends soon. (Summary by Mary Williams @PlantTeaching) Plant Cell 10.1093/plcell/koad127

Update: Callose synthesis in plant development – an evolutionary insight

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Callose is a polysaccharide with amorphous, gel-like properties that often serves as a transient matrix in plant cell walls. Callose deposition at plasmodesmata can regulate the movement of molecules between cells, transient callose deposition in phloem sieve elements occurs in response to stress, callose is deposited at the site at which some pathogens penetrate the host cell, and callose is instrumental in cell plate formation during cytokinesis. The contributions of callose and its synthesis by callose synthases (CalSs) are the focus of this Update by Ušák et a. Callose synthase is a large integral membrane protein encoded by a large gene family. There is some evidence that different family members have different functions. Furthermore, different subclades are more or less abundant across plant and algal lineages. The authors explore CasS phylogeny and expression in light of different forms of cytokinesis (centrifugal cytokinesis versus centripetal cleavage furrow), and highlight several unknowns in our understanding of CalSs in development. (Summary by Mary Williams @PlantTeaching) Plant Physiol. 10.1093/plphys/kiad274

The HOS15-HDA9 complex associates with HYL1 to modulate miRNA expression in response to ABA signalling

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MicroRNAs (miRNAs) play a crucial role in plant cell homeostasis, particularly in response to environmental biotic and abiotic stresses. The transcription of miRNAs is mediated by RNA Polymerase II which generates the primary miRNA transcripts (pri-miRNAs). HYPONASTIC LEAVES 1 (HYL1) is a miRNA biogenesis protein indirectly associated with chromatin through the interaction with the nascent pri-miRNA. HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 15 (HOS15) facilitates the recruitment of histone deacetylases to the promoter of the target genes together with its chromatin-acting partner HISTONE DEACETYLASE 9 (HDA9). Previous works suggest an interaction between the chromatin-remodelling machinery and pri-mRNA processing at transcriptional level. However, the interaction between the HOS15-HDA9 complex together with HYL1 and their functional relevance in ABA signalling remained unclear. In this work, Park et al., show that the ABA-induced recruitment of HOS15-HDA9 complex to the miRNA loci and the following silencing of MIRNA loci depended on the recognition of nascent pri-miRNAs by HYL1. As the authors observe, these findings “indicate that nascent pri-miRNAs serve as scaffolds for recruiting transcriptional regulators, specifically to MIRNA loci.” Understanding theses mechanism is crucial for elucidating the intersection between hormone pathways and epigenetic regulation that fine-tune gene expression in plants. (Summary by Eva Maria Gomez Alvarez @eva_ga96) Plant Cell 10.1093/plcell/koad132