Junbei Ni: The Plant Cell First Author

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Junbei Ni, first author of “The ethylene-responsive transcription factor PpERF9 represses PpRAP2.4 and PpMYB114 via histone deacetylation to inhibit anthocyanin biosynthesis in pear”

Current Position: Associate Professor, College of Agriculture & Biotechnology, Zhejiang University

Education: 2009-2013, Zhejiang University, Bachelor’s degree; 2013-2018, Zhejiang Universtiy, Ph.D

Non-scientific Interests: swimming, flower growing

Brief bio: I developed a strong interest in pear fruit coloration research when I joined into Prof. Yuanwen Teng’s lab in Zhejiang University for undergraduate scientific research training. In September 2013, I joined into Prof. Teng’s lab to conduct my Ph.D. dissertation research. Now I am working in Zhejiang University after finishing my postdoctoral research in Prof. Teng’s lab. In previous studies, we found that the regulation of ethylene on anthocyanin biosynthesis is species-specific. Ethylene induces anthocyanin biosynthesis in most fruits, including apple. However, ethylene inhibits anthocyanin biosynthesis in pear. We found that ethylene can inhibit anthocyanin biosynthesis in pear through several pathways. Firstly, ethylene induces the expression of PpERF105, which induces the expression of the repressive R2R3-MYB transcription factor PpMYB140. PpMYB140 inhibits the expression of key anthocyanin biosynthetic structural genes by forming the repressive M(140)BW complex, and ultimately inhibiting anthocyanin biosynthesis in pear fruit. In addition, ethylene can inhibit anthocyanin biosynthesis through the PpERF9-PpTPL1 corepressor complex-mediated histone deacetylation by inhibiting the expression of PpMYB114 and PpRAP2.4, which are positive regulators of pear anthocyanin biosynthesis. Currently, I’m continuing to investigate the molecular genetic mechanisms underlying the regulation of internal and external quality of pear and mango fruit. We hope that our study can provide a theoretical basis for molecular breeding and quality improvement of pear and mango fruit.

 姓    名：倪隽蓓

发表论文：The ethylene-responsive transcription factor PpERF9 represses PpRAP2.4 and PpMYB114 via histone deacetylation to inhibit anthocyanin biosynthesis in pear

目前职位：浙江大学农业与生物技术学院，副研究员

教育经历：2009-2013，浙江大学，学士；2013-2018，浙江大学，博士

兴趣爱好：游泳，养花

个人简介：我从2011年进入浙江大学农业与生物技术学院滕元文教授实验室进行本科阶段的科研训练，期间对梨果实色泽的研究产生了浓厚的兴趣。2013年9月进入滕元文教授课题组攻读博士学位，博士毕业后在该课题组继续开展博士后工作，博士后出站后留校任副研究员。在前期研究中，我们发现乙烯调控花青苷合成具有种属特异性：乙烯能诱导苹果等大多数果实花青苷的合成；而乙烯抑制梨果实花青苷的合成。我们对此进行了深入研究，发现乙烯能通过多种途径抑制梨果实花青苷的合成：乙烯诱导PpERF105的表达，PpERF105诱导抑制型R2R3-MYB转录因子PpMYB140的表达，PpMYB140则通过形成抑制型M(140)BW复合体抑制花青苷合成关键结构基因的表达，最终抑制梨果皮花青苷合成；此外，乙烯还能通过PpERF9-PpTPL1共抑制复合体介导的组蛋白去乙酰化作用抑制梨花青苷合成正调控转录因子PpMYB114和PpRAP2.4的表达，进而抑制梨果皮花青苷合成。目前，我正在以梨和芒果为研究对象，继续进行果实内在和外在品质的分子遗传控制解析，旨在为梨和芒果的分子育种和性状改良奠定理论基础。

Yongming Chen: The Plant Cell First Author

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Yongming Chen, co-first author of “The translational landscape of bread wheat during grain development”

Current Position: Postdoc in China Agricultural University

Education: PhD in China Agricultural University

Interests: Music, Movie

Brief bio: I received my PhD from China Agricultural University and then joined Wheat Genetics and Genomics Center as a Postdoc. My research now focuses on evolutionary genomics and regulation of gene expression in wheat and its closely related species, as well as the development of tools and databases for omics big data analytics to accelerate crop improvement. In previous work, I developed a collinearity-incorporating homology inference tool and a homology database for Triticeae species and constructed a wheat integrative regulatory network that enables trait-associated gene discovery for crop improvement. In this study, we generated a unique translatome dataset of developing bread wheat grain using ribosome profiling and polysome profiling and presents a comprehensive and detailed overview of the translational control of gene expression, facilitating molecular designed breeding for crop improvement.

 陈永明

目前职位：中国农业大学，博士后

教育背景：中国农业大学，博士

兴趣爱好：音乐，电影

个人简介：在中国农业大学获得博士学位后，我继续在小麦研究中心进行博士后研究。我主要进行小麦及其近缘种的进化基因组学和基因表达调控研究，并开发组学大数据分析工具以加速作物改良。在之前的工作中，我开发了基于共线性的同源基因推断方法及小麦族同源基因数据库，构建了用于功能基因发掘的小麦整合基因调控网络。在该研究中，我们利用核糖体谱和多聚核糖体谱分析技术获得了小麦籽粒发育翻译组图谱，全面解析了基因表达的翻译调控机制，为小麦精准设计育种提供了理论基础。

Yiwen Guo: The Plant Cell First Author

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Yiwen Guo, co-first author of “The translational landscape of bread wheat during grain development”

Current Position: Ph.D. candidate in China Agricultural University

Education: Bachelor, Northeast Forestry University

Interests: Travel, Photography, Reading

Brief bio: During the undergraduate period, I developed a strong interest in molecular biology and began to conduct scientific research training in the laboratory. I joined Wheat Genetics and Genomics Center at CAU since 2018 to pursue my Ph.D. My research mainly focuses on the translational regulatory mechanism of wheat and the functions and regulatory mechanisms of translational regulatory elements such as uORFs. In this study, we performed ribosome profiling and polysome profiling to obtain a unique translatome dataset of developing bread wheat grain. The study provides the first comprehensive and detailed overview of the translational regulations affecting gene expression during wheat grain development, providing a theoretical basis for wheat improvement.

郭译文

目前职位：中国农业大学博士研究生

教育经历：东北林业大学本科

兴趣爱好：旅行，摄影，阅读

个人简介：从本科阶段我就对分子生物学产生了浓厚的兴趣，并开始在实验室进行科研训练。2018年，我有幸加入中国农业大学攻读硕士学位，并加入小麦研究中心，于2020年开始博士生涯。我主要的研究方向是小麦的翻译调控机制，并对uORF等翻译调控元件的功能及调控机制进行解析。在本研究中，我们利用核糖体谱分析和多聚核糖体谱分析构建了面包小麦籽粒不同发育阶段的翻译调控图谱，并对小麦籽粒发育中的翻译调控进行了全面和详细的阐述，为小麦高产优质品种改良提供理论基础。

Ahmed Alabd: Plant Physiology First Author

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Ahmed Alabd, first author of “ABRE-BINDING FACTOR3-WRKY DNA-BINDING PROTEIN44 module promotes salinity-induced malate accumulation in pear”

Current position:

Ph.D. Candidate at College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China

Education:

2018-now: Ph.D. student, Zhejiang University, Hangzhou, China;

20??-2016: M.Sc. Alexandria University, Egypt;

20??-2011: B.Sc. Alexandria University, Egypt.

Non-scientific interest:

Playing and watching sports, reading and cooking

Brief bio:

I’m currently studying at the College of Agriculture and Biotechnology, Zhejiang University, China. Since joining Prof Yuanwen Teng’s lab in 2018, I have been conducting research on the regulatory mechanisms of anthocyanins and malic acid in fruits under the supervision of of Prof Yuanwen Teng, Dr Songling Bai and Dr Junbei Ni. In this research, we revealed a regulatory mechanism by which salinity affects malate accumulation. Genetic and biochemical analyses showed the key roles of PpWRKY44 and ABRE-BINDING FACTOR3 (PpABF3) transcription factors in promoting malate accumulation in response to salinity. We found that PpWRKY44 is involved in salinity-induced malate accumulation by binding directly to the W-box on the promoter of the malate-associated gene PpALMT9 (aluminium-activated malate transporter 9) to activate its expression. A series of in vivo and in vitro assays showed that the G-box cis-element in the promoter of PpWRKY44 was targeted by PpABF3, which further enhanced salinity-induced malate accumulation. This research provides new insights into the regulatory mechanism of malate accumulation in pear fruit in response to salinity.

我目前在中国浙江大学农业与生物技术学院学习。自2018年进入滕元文教授实验室以来，我在滕元文教授、白松龄博士和倪隽蓓博士的指导下，开展了水果中花青苷和苹果酸的调控机制研究。在这项研究中，我们揭示了盐胁迫影响苹果酸积累的调控机制。遗传和生化分析表明，PpWRKY44和ABRE-BINDING FACTOR3（PpABF3）转录因子在促进苹果酸盐积累中发挥了关键作用。我们发现，PpWRKY44通过直接与苹果酸相关基因PpALMT9（铝激活的苹果酸转运体9）启动子上的W-box结合，激活其表达，从而参与盐分诱导的苹果酸盐积累。一系列体内和体外实验表明，PpABF3与PpWRKY44启动子中的G-box顺式元件结合，进一步增强了盐胁迫诱导的苹果酸积累。该研究为梨果实应对盐胁迫的苹果酸积累的调控机制提供了新见解。

Xiaoping Xu: Plant Physiology First Author

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Xiaoping Xu, first author of “Riboflavin mediates m6A modification targeted by miR408, promoting early somatic embryogenesis in longan”

Current Position: Research assistant, Institute of biotechnology Research, Fujian Academy of Agricultural Sciences, Fuzhou, China

Education: 2012.09-2016.06, Fujian Agriculture and Forestry University (bachelor); 2016.09-2022.06, Fujian Agriculture and Forestry University (PhD).

Non-scientific interests: Reading, Playing badminton and volleyball

Brief bio: I am currently working in Biotechnology Institute of Fujian Academy of Agricultural Sciences. I was fortunate to be guided by Prof. Zhongxiong Lai and Prof. Yuling Lin from the College of Horticulture, Fujian Agriculture and Forestry University. I have been studying the mechanism of miR408 in the process of early somatic embryogenesis (SE) of longan since my postgraduate study in 2016. The related research results have been published in Scientific Report (2020), Journal of Plant Physiology (2021), Plant science (2022), and Plant physiology (2023). This study optimized the SE transgene regeneration system of longan to achieve embryogenic callus (EC) transformation of longan to induce somatic embryogenesis, verifying the function of embryonic development genes, thus solving the problem of long verification period of gene function in the process of embryonic development in woody plants. This study revealed dlo-miR408-3p-DlNUDT23-FMN-m6A model promoting the division and differentiation of early embryonic cells of longan, and provided new insights into the molecular mechanism of miR408 in early SE of longan and other plants.

My collaborators and I are very honored and pleased to have this article published in Plant Physiology.

 

第一作者姓名：徐小萍

目前职位：福建省农业科学院生物技术研究所，助理研究员

教育经历：2012.09-2016.06，福建农林大学园艺学院（学士）；

2016.09-2022.06，福建农林大学园艺学院（硕博连读）

2022.09-至今，福建省农业科学院

兴趣爱好：阅读、羽毛球、排球

个人简介：本人目前就业于福建省农业科学院生物技术研究所。自2016年研究生入学以来有幸一直在福建农林大学园艺学院赖钟雄研究员与林玉玲教授的指导下开展miR408在龙眼体胚发生早期的作用机制研究。相关研究成果发表在Scientific Report（2020）、Journal of Plant Physiology（2021）、Plant science（2022）、和Plant physiology（2023）上。本研究优化龙眼SE转基因再生体系，实现转基因龙眼胚性愈伤组织（embryogenic callus，EC）诱导体胚发生，进而验证胚胎发育基因的功能，解决了木本植物胚胎发育过程基因功能验证周期长的难题。本研究揭示了dlo-miR408-3p-DlNUDT23-FMN-m6A模型促进龙眼早期胚性细胞分裂分化的作用机制，为miR408在龙眼及其他植物体胚发生中的分子机制研究提供新的思路。我和我的合作者为这篇文章发表在Plant Physiology上感到十分荣幸和由衷地高兴。

Lignin chemistry is fine-tuned on the nanoscale by different combinations of LACCASES

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Blaschek et al. explore the spatial control of lignin chemistry.

Leonard Blaschek1 and Edouard Pesquet1,2,3

1 Department of Ecology, Environment and Plant Sciences (DEEP), Stockholm University, 106 91 Stockholm, Sweden

2 Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden

3 Bolin Centre for Climate Research, Stockholm University, 106 91 Stockholm, Sweden

Background: Lignins are a diverse, complex group of aromatic polymers that accumulate in cell walls of vascular plants, reinforcing organs and enabling long-distance water transport. The different cell wall layers of each cell type exhibit specific lignin chemistries with distinct proportions of specific aromatic substitutions and aliphatic functions. The spatial control of this lignin chemistry was supposed to depend exclusively on the chemical identity of the lignin monomers exported into the cell wall. However, monomer supply alone cannot fully explain the sharp spatial differences between each cell wall layer in the different cell types. We therefore investigated whether different paralogs of the lignin monomer-oxidizing LACCASE enzymes are responsible for spatially controlling lignin chemistry at the cell wall layer level for the different cell types in the vascular tissues of plants.

Question: How are specific lignin chemistries spatially controlled by LACCASE paralogs in each cell wall layer and cell type? What are the roles of LACCASE-dependent lignin accumulation for the mechanical reinforcement and the waterproofing of different cell types in plant vascular tissues?

Findings: We answered these questions by identifying the LACCASE paralogs specifically expressed in vascular cells undergoing lignin accumulation. We analyzed their functions using genetic engineering to switch off five of the six LACCASE paralog genes associated with lignin formation. Their importance in the cell wall layer and cell type lignin accumulation was determined by comparing plants sharing four of the five mutations in different LACCASE paralogs. We show that each LACCASE paralog exhibits specific substrate preference, pH optimum and localization differing between the cell wall layers of each cell type. Their lignin concentration and composition moreover depended on specific combinations of LACCASE paralogs, each enabling different aromatic substitutions and aliphatic functions to accumulate. Impairing these LACCASE-dependent lignin chemistries resulted in the loss of cell wall mechanical resistance of sap-conducting cells and the loss of cell wall waterproofing of organ-reinforcing fiber cells.

Next steps: We are now pursuing research to understand the molecular mechanisms controlling the supply of lignin precursors as well as the temporal regulation activating lignification during the formation/maturation of each cell wall layer in the different cell types.

Reference:

Leonard Blaschek, Emiko Murozuka, Henrik Serk, Delphine Ménard, Edouard Pesquet. (2023). Different combinations of laccase paralogs nonredundantly control the amount and composition of lignin in specific cell types and cell wall layers in Arabidopsis. https://doi.org/10.1093/plcell/koac344

MtNRT2.1 controls root nodule formation in response to the ambient nitrate concentration

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Luo et al. investigate how nitrate transporters direct root nodule formation in a legume.

By Zhenpeng Luo & Fang Xie

CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.

 Background: Nitrogen (N) is an essential nutrient and signaling molecule for plant growth and development. Legume plants can not only use N from soil as nitrate (NO3–), but also obtain N through symbiotic nitrogen fixation with bacteria (rhizobia), which inhabit nodules formed on the plant roots. However, nodule formation and nitrogen fixation are energy-consuming processes for plants; therefore, plants control nodule formation depending on the concentration of available nitrate. High concentrations of nitrate inhibit nodule formation and low concentrations of nitrate promote nodule formation. However, how nitrate controls nodulation remains unclear.

Question: How do the legume nitrate transporters (NRTs) responsible for the uptake/transport of low/high nitrate control root nodule formation in Medicago truncatula?

Findings: Here we report that M. truncatula MtNRT2.1 has both high- and low-affinity nitrate uptake transport activity, and MtNRT2.1 is required for optimal nodule establishment under low nitrate and inhibiting nodulation when nitrate is sufficient. We showed that the transcription factor MtNLP1 directly activated MtNRT2.1 expression and regulation of nitrate uptake under low- and high-nitrate. Under low nitrate, the gene encoding the small peptide MtCEP1 was highly expressed, and the application of this peptide systemically promoted MtNRT2.1 expression in a MtCRA2-dependent manner. MtNRT2.1 is required for the peptide MtCEP1 to enhance nodulation and nitrate uptake. Our study demonstrates that nitrate uptake by MtNRT2.1 differentially affects nodulation under low- and high-nitrate conditions and this is controlled by MtCEP1 and MtNLP1.

Next steps: Soil N uptake and symbiotic N are important for the growth and yield of legume crops, including soybean (Glycine max). Evaluating the conservation of the mechanisms identified in Medicago may provide insight on other legumes in the future.

Zhenpeng Luo, Jiang Wang, Fuyu Li, Yuting Lu, Zijun Fang, Mengdi Fu, Kirankumar S. Mysore, Jiangqi Wen, Jiming Gong, Jeremy D. Murray and Fang Xie. (2023). The small peptide CEP1 and the NIN-like protein NLP1 regulate NRT2.1 to mediate root nodule formation across nitrate concentrations. https://doi.org/10.1093/plcell/koac340

Review: Proximity labeling in plants

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Genetic studies can suggest that two proteins function in the same pathway, but how can we figure out if they share the same space? In this review, Xu et al. provide an overview of proximity labeling, a method to identify proteins that co-localize in space. Proximity labeling uses a biotin ligase which is incubated with biotin to produce short-lived diffusible biotin adenylate intermediates. These tags are transferred to proteins within a very narrow (10nm) radius, and then the labeled proteins can be captured by streptavidin beads and identified through mass spectrometry; it’s a bit like throwing a tiny net into the cell and analyzing what is caught associating with what. The ligase can be fused to a protein of interest (bait) to search for its interactors, or targeted to an organelle, or expressed from a cell-specific promoter to query specific proteomes. These approaches have been enhanced by directed engineering of the biotin kinase enzyme to make it work faster, resulting in enzymes such as TurboID that can carry out proximity labeling in as little as ten minutes. This review focuses on the application of these methods in plants. (Summary by Mary Williams @PlantTeaching) Annu. Rev. Plant Biol. 10.1146/annurev-arplant-070522-052132

Review. Climate change impacts on seed production and quality

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As the effects of climate change become increasingly severe and evident, there is growing concern about the future of food production. However, unlike its impact on crop yields, there is little clarity on the effects of climate change on the foundation of most agricultural systems: seed production and quality. In this paper, Maity and colleagues provide a detailed review of how climate change can affect the different phases of seed development and the seed supply chain. They focus on four abiotic factors: temperature, precipitation, CO2 concentration and UV radiation. An analysis with a selected crop pool indicates that some groups of plants’ seed yield and quality might be more susceptible to climate change, such as annuals, monocots and self-pollinated species. Still, the authors highlight the need for a more comprehensive quantitative analysis to assess the extent and magnitude of such impacts. Various strategies to potentially minimize the adverse effects of climate change are outlined, including seed enhancement technologies and directed breeding schemes. Given this, this review should be a primer for those interested in better understanding the effects of climate change on the seed industry and the alternative to deal with it. (Summary by Carlos A. Ordóñez-Parra @caordonezparra) Seed Sci. Technol. 10.15258/sst.2023.51.1.07