ZmNAC128 and ZmNAC130 coordinate with Opaque2 to promote endosperm filling in maize

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Chen, Yu, He, Peng et al. investigate the synchronized mechanisms of endosperm filling, from nutrient uptake to the biosynthesis of storage reserves.

https://doi.org/10.1093/plcell/koad215

By Di Peng and Zhiyong Zhang

School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China

 Background: Cereal endosperms store starch and proteins in grains and play a critical role in determining grain yield and quality. Maize (Zea mays), with its sizable grain, is an excellent model for studying cereal endosperm development. Endosperm filling involves two synchronized processes: maternal-to-endosperm nutrient transfer and storage reserve biosynthesis. Several important nutrient transfer-related genes have been identified, and the regulation of storage reserve biosynthesis has been broadly studied in maize. Notably, the transcription factor-encoding genes Opaque2 (O2), ZmNAC128, and ZmNAC130 exhibit strong expression in the filling endosperm. However, how these three transcription factors co-regulate the synchronization of these endosperm-filling processes remains elusive.

 Question: What are the roles of ZmNAC128 and ZmNAC130 in endosperm filling? How do they function together with O2 in this process?

Findings: ZmNAC128 and ZmNAC130 directly regulate the expression of all γ-zein genes (encoding storage proteins) and multiple important starch metabolism genes, making them pivotal coordinators of grain quality and yield. Furthermore, ZmNAC128 and ZmNAC130 directly regulate the expression of O2, and together these three transcription factors synergistically activate their own expression through autoregulation and physical interactions. ZmNAC128 and ZmNAC130 also regulate the expression of vital transporter genes responsible for facilitating nutrient transfer from the mother plant to the endosperm. This regulatory mechanism enhances nutrient uptake, with O2 playing a supportive role.

Next steps: We plan to identify additional co-regulatory factors involved in endosperm filling to gain a comprehensive understanding of endosperm filling, from nutrient uptake to the biosynthesis of storage reserves.

Reference:

Erwang Chen, Huiqin Yu, Juan He, Di Peng, Panpan Zhu, Shuxing Pan, Xu Wu, Jincang Wang, Chen Ji, Zhenfei Chao, Zhuopin Xu, Yuejin Wu, Daiyin Chao, Yongrui Wu and Zhiyong Zhang (2023). Transcription factors ZmNAC128 and ZmNAC130 coordinate with OPAQUE2 to promote endosperm filling in maize. https://doi.org/10.1093/plcell/koad215

A transcriptional network that controls strawberry fruit ripening

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Xiaojing Li and Guozheng Qin, Institute of Botany, Chinese Academy of Sciences

Background: Strawberry is an important horticultural crop with a high economic value worldwide. Various factors regulate the ripening of strawberry fruit, including the plant hormone abscisic acid (ABA), epigenetic modifications, and transcription factors. In a previous study, the transcription factor Ripening Inducing Factor (RIF) was reported to be necessary for the ripening of strawberry fruit, but the regulatory network mediated by RIF remains unclear.

Question: What are the direct target genes of RIF in strawberry? How is the transcriptional activity of RIF modulated?

Findings: We found that RIF in diploid strawberry (Fragraria vesca, FvRIF) functions as a key regulator in controlling fruit ripening, and loss of function of FvRIF leads to a complete blockage of the ripening process. DNA affinity purification sequencing coupled with RNA sequencing identified 2080 genes as potential direct targets of FvRIF, including genes involved in anthocyanin biosynthesis, cell wall degradation, and sugar metabolism. We demonstrate that FvRIF regulates various aspects of fruit ripening by directly modulating core sets of genes involved in these processes. Furthermore, we show that FvRIF physically interacts with the kinase FvMAPK6, which phosphorylates and regulates FvRIF activity.

Next steps: We next wish to identify the transcription factors that directly bind to the promoter of FvRIF and regulate its expression. Moreover, our work suggests a number of transcription factors as the targets of FvRIF. It will be interesting to explore their function in the regulation of strawberry fruit ripening.

Reference: 

Xiaojing Li, Carmen Martín-Pizarro, Leilei Zhou, Bingzhu Hou, Yuying Wang, Yuanyue Shen, Bingbing Li, David Posé, Guozheng Qin (2023) Deciphering the regulatory network of the NAC transcription factor FvRIF, a key regulator of strawberry (Fragaria vesca) fruit ripening. https://doi.org/10.1093/plcell/koad210

A CRISPRi library screen reveals growth-robustness tradeoffs in Synechocystis

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Miao & Jahn et al. generated and screened a large CRISPRi-based library of Synechocystis in 11 different growth conditions to reveal growth-robustness tradeoffs and to discover genes with condition specific importance and additional functions.

https://doi.org/10.1093/plcell/koad208

By  Rui Miao1, Michael Jahn1,2, and Elton P. Hudson1

1School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH – Royal Institute of Technology, Stockholm, Sweden.

2Max Planck Unit for the Science of Pathogens, Berlin, Germany.

 Background: Cyanobacteria are photosynthetic microbes that play a crucial role in the global carbon cycle. They convert sunlight into chemical energy and produce oxygen as a byproduct. Extant cyanobacteria are also thought to share a common ancestor with the chloroplasts of plants and algae. However, nearly half of the genes in model cyanobacteria strains are not annotated with a function. This knowledge gap is a significant obstacle for fully understanding the physiology of photosynthesis, as well as for developing cyanobacteria into efficient cell factories for bioproduction.

Question: We aimed to map whether genes in cyanobactera are essential and contribute to cell fitness different growth conditions spanning a wide range of light regimes and carbon source availabilities.

Findings: We screened a large gene repression library consisting of more than 20,000 individual mutants in 11 different conditions. We found that certain genes showed fitness benefits in one condition but were generally detrimental in others, including several genes that play critical roles in mixotrophy and photoheterotrophy, indicating their significance in redirecting metabolic flux. We also discovered genes with condition-specific importance and identified additional functions for central metabolic enzymes. We compiled the fitness data for all genes in all conditions in an interactive, open access web application. In addition, we used our extensive dataset in combination with machine learning to identify “design rules” for effective guide RNAs in the cyanobacterium Synechocystis.

Next steps: Our results provide important insight to the cyanobacteria community, and to plant scientists looking for cyanobacterial homologues to chloroplast proteins or other examples of suboptimality in regulation of photoprotection. Future studies may focus on investigating the highlighted genes or regulatory pathways with individual mutants.

Rui Miao, Michael Jahn, Kiyan Shabestary, Gilles Peltier, Elton Paul Hudson. (2023). CRISPR interference screens reveal growth–robustness tradeoffs in Synechocystis sp. PCC 6803 across growth conditions. https://doi.org/10.1093/plcell/koad208

Review: Paternal imprinting in Marchantia polymorpha

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Humans and flowering plants spend most of their lives in a diploid state with two copies of each chromosome in most cells, but to reproduce they produce haploid gametes through meiosis. By contrast, bryophytes (liverworts, hornworts, and mosses), spend most of their lives in the haploid state. They produce gametes through mitosis and differentiation, and then very briefly experience a diploid state before meiosis leads again to the dominant, haploid state. The process of toggling between diploid and haploids is actually quite complicated, as some genes should only be active in one state or the other, or when inherited from one parent or the other. Shutting off of specific genes by parent-of-origin is known as imprinting, and usually involves the polycomb repressive complex and histone methylation (H3K27me3). Recently, Montgomery and Berger and colleagues identified a new type of selective gene silencing in the liverwort Marchantia, which involves the complete silencing of the paternal genome for the duration of the diploid stage – effectively rendering it haploid. This review discusses this novel finding in the context of other forms of imprinting and the evolution of land plants. Check it out! (Summary by Mary Williams @PlantTeaching) New Phytol. doi.org/10.1111/nph.19377

Review: The exocyst complex is targeted by pathogen effectors

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The exocyst complex is a conserved octameric protein complex in eukaryotic cells. Its primary function is to tether secretory vesicles to the plasma membrane during the exocytosis process, and it is also involved in autophagy and host-pathogen interactions. Intriguingly, EXO70, one of the subunits of the exocyst complex, is present in a single copy in animals and fungi, but has expanded into a large protein family in plants. In a recent review, De la Concepcion brings together current research about the exocyst complex, including its 3D structure and investigations into the functional diversification of EXO70 in plants. Most notably, the review focuses on the different ways that the exocyst complex helps plants combat pathogens, for example through direct or indirect interactions with immune proteins. Not surprisingly given its role in immunity, the exocyst complex is targeted by several pathogen effectors, which are summarized in a useful table listing pathogen effectors and their targeted exocyst subunits. The review ends by raising open important questions about the diversification of exocyst subunits and pathogen effector–exocyst interactions. (Summary by Xiaohui Li @Xiao_hui_Li) Curr. Opin. Plant Biol. 10.1016/j.pbi.2023.102482. (For further insights into the exocyst complex’s role in autophagy, refer to Viktor Žárský’s detailed review in FEBS Letters 10.1002/1873-3468.14430.)

Review: CLAVATA signaling in plant-environment interactions

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CLAVATA 3/EMBRYO SURROUNDING REGION-related (CLE) peptides and CLAVATA type receptors have been well charecterized for their role in root and shoot apical meristem maintenance in Arabidopsis. CLE peptides are also referred to as “peptide hormones” for their role in contolling physiological and developmental changes in plants. In this review by Bashyal et al., the roles of these peptides in regulating plant responses to various environmental stimuli is comprehensively summarized. CLAVATA signaling has diverse roles ranging from plant developmental adaptations to nutrient availability, responses to abiotic and biotic stimuli, and symbiotic relationships with rhizobia and arbuscular mycorrhiza fungi. The review also describes interesting studies on CLE-like signaling peptides from parasitic nematodes that hijack the plant-CLAVATA signaling pathway for their own benefit. The authors anticipate that future functional characterization through advanced bioinformatic tools will help in understanding how CLE-specific plant responses integrate plant physiology and the environment. (Summary by Indrani Kakati  @Indranik333) Plant Physiol. 10.1093/plphys/kiad591

Review: Increasing yields of barley and wheat through inflorescence architecture

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The Triticeae is an important tribe of crops that contains both barley and wheat. As the global population increases, the yield of Triticeae crops must increase to meet global food demands. An important factor influencing yield is grain number per spike, which is affected by inflorescence architecture. Here, Zhang et al. suggest that altering the inflorescence architecture in Triticeae crops by increasing the amount of branching and the number of spikelets per inflorescence could lead to higher yields. They highlight many key regulators that could be targeted to achieve this, for instance the AP2-ERF (APETALA2/ETHYLENE RESPONSIVE FACTOR) transcription factor COMPOSITUM 2 in barley which when mutated results in a highly branched spike. Another potential target is the miRNA156-SPL (SQUAMOSA promoter binding protein-like) module; SPL knockout wheat lines have decreased spikelet number, so increasing SPL expression might increase spikelet number. Such regulators could be targeted using CRISPR/Cas9 genome editing or by searching for beneficial alleles in seed stores or wild relatives, leading to increased yields of these important crops. (Summary by Rose McNelly @rose_mcn) J. Exp. Bot. 10.1093/jxb/erad386

RALF4 prevents pollen tubes from growing crazy

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Pollen tubes are characterized by extremely fast elongation growth. Previously, small peptides known as RALFs (RAPID ALKALINIZATION FACTORs) were identified as signaling peptides, some with a role in pollen tube growth; for instance, RALF4/19 are important in maintaining the cell wall integrity of pollen tubes. RALF peptides bind to a membrane-integral protein complex consisting of LLGs [LORELEI-like GLYCOLPHOSPHATIDYLINOSITOL (GPI)-ANCHORED PROTEINS] and CrRLK1Ls (Catharanthus roseus RLK1-like receptor kinases). In addition, RALF peptides also bind to cell wall-anchored LRX (LEUCINE-RICH REPEAT EXTENSIN) proteins. When RALF4 binds to LRX8, it exposes an alkaline surface patch hypothesized to interact with negatively charged cell wall polysaccharides like pectin. In a recent study, Moussu et al. used the Arabidopsis pollen tube to explore the LRX8-RALF4 complex’s role in cell wall patterning. Using biochemical assays, they discovered that the LRX8-RALF4 complex directly binds to oligogalacturonans (OGs, a type of pectin). Notably, neither RALF4 nor LRX8 alone could bind to OGs independently. This interaction is specific to demethylated pectins, found predominantly in the pollen tube’s shank. Super-resolution imaging with immunolabeling revealed that LRX8 and RALF4 not only colocalize but also associate with pectin, creating a reticulated pattern along the pollen tube cell wall. Surprisingly, RALF4 is present along the pollen tube cell wall as an integral component colocalizing with LRX8. In addition, they found that mutations of the exposed alkaline surface of RALF4 lead to abnormal cell wall patterning, increased pollen tube growth rates, and premature bursting. Collectively, these discoveries highlight the critical role of the LRX8-RALF4-pectin association in the assembly and patterning of the pollen tube cell wall. (Summary by Xiaohui Li @Xiao_hui_Li) Science 10.1126/science.adi4720. For an extended analysis of this study’s background and future directions, and to see a wonderful image of pectin network in an Arabidopsis pollen tube, I recommend to read the excellent perspective article from Debra Mohnen in Science (10.1126/science.adl1198).

Lateral root branching promoted by ammonia borane-dependent H2

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Molecular hydrogen (H2) has been shown to have several cellular benefits, most notably serving as an antioxidant. Its effects in humans and plants have been primarily assayed using hydrogen-rich water (HRW, produced by bubbling H2 into water), but slower, more persistent release of H2 has been demonstrated from solid ammonia borane (NH3BH3). Here, Wang et al. examined how ammonia borane affects root growth, using hydroponically grown tomatoes treated with ammonia borane (AB). Upon treatment with AB, roots showed an increase in expression level of several genes involved in the synthesis of phytomelatonin and an accompanying increase in phytomelatonin levels. The AB-promoted increase in root branching is suppressed by an inhibitor of phytomelatonin synthesis, and root branching is enhanced by exogenous phytomelatonin treatment, suggesting that the effects of AB are mediated through phytomelatonin. AB or phytomelatonin further led to an increase in expression on several auxin-signaling genes, suggesting that auxin has a role in this response. (Summary by Mary Williams @PlantTeaching) Plant Physiol. 10.1093/plphys/kiad595