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Authors: Byron Rusnak, Frances K. Clark, Batthula Vijaya Lakshmi Vadde and Adrienne H.K. Roeder.
Annual Review of Cell and Developmental Biology (2024)
Abstract: "One of the fundamental questions in developmental biology is how a cell is specified to differentiate as a specialized cell type. Traditionally, plant cell types were defined based on their function, location, morphology, and lineage. Currently, in the age of single-cell biology, researchers typically attempt to assign plant cells to cell types by clustering them based on their transcriptomes. However, because cells are dynamic entities that progress through the cell cycle and respond to signals, the transcriptome also reflects the state of the cell at a particular moment in time, raising questions about how to define a cell type. We suggest that these complexities and dynamics of cell states are of interest and further consider the roles signaling, stochasticity, cell cycle, and mechanical forces play in plant cell fate specification. Once established, cell identity must also be maintained. With the wealth of single-cell data coming out, the field is poised to elucidate both the complexity and dynamics of cell states."
Authors: Fuxi Rong, Yusong Lv, Pingchuan Deng, Xia Wu, Yaqi Zhang, Erkui Yue, Yuxin Shen, Sajid Muhammad, Fangrui Ni, Hongwu Bian, Xiangjin Wei, Weijun Zhou, Peisong Hu and Liang Wu.
Nature Communications (2024)
Editor's view: miR408-5p typically regulates target IAA30 via translation repression, but switches to cleaving IAA30 mRNA under high auxin conditions. miR393, miR156, miR408-5p and their targets could hierarchically act in auxin pathway and regulate leaf inclination.
Abstract: "MicroRNAs (miRNAs) play fundamental roles in many developmental and physiological processes in eukaryotes. MiRNAs in plants generally regulate their targets via either mRNA cleavage or translation repression; however, which approach plays a major role and whether these two function modes can shift remains elusive. Here, we identify a miRNA, miR408-5p that regulates AUXIN/INDOLE ACETIC ACID 30 (IAA30), a critical repressor in the auxin pathway via switching action modes in rice. We find that miR408-5p usually inhibits IAA30 protein translation, but in a high auxin environment, it promotes the decay of IAA30 mRNA when it is overproduced. We further demonstrate that IDEAL PLANT ARCHITECTURE1 (IPA1), an SPL transcription factor regulated by miR156, mediates leaf inclination through association with miR408-5p precursor promoter. We finally show that the miR156-IPA1-miR408-5p-IAA30 module could be controlled by miR393, which silences auxin receptors. Together, our results define an alternative auxin transduction signaling pathway in rice that involves the switching of function modes by miR408-5p, which contributes to a better understanding of the action machinery as well as the cooperative network of miRNAs in plants."
Authors: Edgar Demesa-Arevalo, Madhumitha Narasimhan and Rüdiger Simon.
Annual Review of Plant Biology (2024)
Abstract: "The shoot meristem of land plants maintains the capacity for organ generation throughout its lifespan due to a group of undifferentiated stem cells. Most meristems are shaped like a dome with a precise spatial arrangement of functional domains, and, within and between these domains, cells interact through a network of interconnected signaling pathways. Intercellular communication in meristems is mediated by mobile transcription factors, small RNAs, hormones, and secreted peptides that are perceived by membrane-localized receptors. In recent years, we have gained deeper insight into the underlying molecular processes of the shoot meristem, and we discuss here how plants integrate internal and external inputs to control shoot meristem activities."
Authors: Leticia F. Ferigolo, Mateus H. Vicente, Joao P. O. Correa, Carlos H. Barrera-Rojas, Eder M. Silva, Geraldo F. F. Silva, Airton Carvalho Jr, Lazaro E. P. Peres, Guilherme B. Ambrosano, Gabriel R. A. Margarido, Robert Sablowski and Fabio T. S. Nogueira.
Development (2023)
Summary: Tomato floral meristem determinacy and fruit development are both orchestrated by the interplay between gibberellin and microRNA156-targeted SlSBP genes.
Abstract: "Many developmental processes associated with fruit development occur at the floral meristem (FM). Age-regulated microRNA156 (miR156) and gibberellins (GAs) interact to control flowering time, but their interplay in subsequent stages of reproductive development is poorly understood. Here, in tomato (Solanum lycopersicum), we show that GA and miR156-targeted SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL or SBP) genes interact in the tomato FM and ovary patterning. High GA responses or overexpression of miR156 (156OE), which leads to low expression levels of miR156-silenced SBP genes, resulted in enlarged FMs, ovary indeterminacy and fruits with increased locule number. Conversely, low GA responses reduced indeterminacy and locule number, and overexpression of a S. lycopersicum (Sl)SBP15 allele that is miR156 resistant (rSBP15) reduced FM size and locule number. GA responses were partially required for the defects observed in 156OE and rSBP15 fruits. Transcriptome analysis and genetic interactions revealed shared and divergent functions of miR156-targeted SlSBP genes, PROCERA/DELLA and the classical WUSCHEL/CLAVATA pathway, which has been previously associated with meristem size and determinacy. Our findings reveal that the miR156/SlSBP/GA regulatory module is deployed differently depending on developmental stage and create novel opportunities to fine-tune aspects of fruit development that have been important for tomato domestication."
Authors: Meiqi Zhao, Yijing Lei, Ling Wu, Haoran Qi, Zihe Song and Meng Xu.
The Plant Journal(2024)
Significance Statement: The non-coding small RNA, miR159a, promotes poplar adventitious root (AR) growth by down-regulating the transcription level of PeMYB33, which provides a reference for further understanding of the regulatory mechanism of AR formation in woody plants.
Abstract: "As sessile organisms, plants experience variable environments and encounter diverse stresses during their growth and development. Adventitious rooting, orchestrated by multiple coordinated signaling pathways, represents an adaptive strategy evolved by plants to adapt to cope with changing environmental conditions. This study uncovered the role of the miR159a-PeMYB33 module in the formation of adventitious roots (ARs) synergistically with abscisic acid (ABA) signaling in poplar. Overexpression of miR159a increased the number of ARs and plant height while reducing sensitivity to ABA in transgenic plants. In contrast, inhibition of miR159a (using Short Tandem Target Mimic) or overexpression of PeMYB33 decreased the number of ARs in transgenic plants. Additionally, miR159a targets and cleaves transcripts of PeMYB33 using degradome analysis, which was further confirmed by a transient expression experiment of poplar protoplast. We show the miR159a-PeMYB33 module controls ARs development in poplar through ABA signaling. In particular, we demonstrated that miR159a promotes the expression of genes in the ABA signaling pathway. The findings from this study shed light on the intricate regulatory mechanisms governing the development of ARs in poplar plants. The miR159a-PeMYB33 module, in conjunction with ABA signaling, plays a crucial role in modulating AR formation and subsequent plant growth."
Authors: Sonia Balyan, Deepika Sharma, Shivani Kansal, Vaishali Panwar, Ringyao Jajo, Tonu Angaila Chithung and Saurabh Raghuvanshi.
bioRxiv (2023)
Abstract: "miRNAs are a critical component of regulatory mechanisms involved in plant growth, development, and stress response including phytohormone action. The role of miRNAs in regulating the strigolactone (SL) signaling in plants is still unexplored. Here we report that miR528 impacts the SL signaling via the post-transcriptional regulation of Dwarf 3 (OsD3). Comparative miRNome analysis under drought conditions in flag leaf, inflorescence, and roots uncovered the tissue-biased unique stress response of miR528 in drought-tolerant N22 (down in inflorescence and roots; up in flag leaf). Consequently, its target, OsD3 which encodes for the F-BOX/LRR-REPEAT MAX2 HOMOLOG and is a critical component of the rice SL signaling pathway exhibit opposite expression to miR528 in all three tissues. Interestingly, OsD3 is a rice-specific target of miR528. miR528 overexpression plants exhibited early heading, increment in the number of tillers, flag leaf length, and width, number of panicle branches, grain per panicle, effective grains per panicle, seed length, and photosynthesis rate. miR528 overexpression plants exhibited similar traits to Osd3 mutants including high tiller number, root architecture under low nitrogen conditions, and moderate insensitivity to GR24 and TIS1 levels in addition to shared transcriptional regulation. Furthermore, SL (GR24) negatively impacts the miR528 transcription. The impact of the miR528:D3 module is also reflected in the D53-mediated downstream signaling involving IPA1 regulon."
Authors: Monika Dalal, Mansi and Karthikeyan Mayandi.
Planta (2023)
Main conclusion: The review describes tissue-specific and non-cell autonomous molecular responses regulating the root system architecture and function in plants.
Abstract: "Phenotypic plasticity of roots relies on specific molecular and tissue specific responses towards local and microscale heterogeneity in edaphic factors. Unlike gravitropism, hydrotropism in Arabidopsis is regulated by MIZU KUSSIE1 (MIZ1)-dependent asymmetric distribution of cytokinin and activation of Arabidopsis response regulators, ARR16 and ARR17 on the lower water potential side of the root leading to higher cell division and root bending. The cortex specific role of Abscisic acid (ABA)-activated SNF1-related protein kinase 2.2 (SnRK2.2) and MIZ1 in elongation zone is emerging for hydrotropic curvature. Halotropism involves clathrin-mediated internalization of PIN FORMED 2 (PIN2) proteins at the side facing higher salt concentration in the root tip, and ABA-activated SnRK2.6 mediated phosphorylation of cortical microtubule-associated protein Spiral2-like (SP2L) in the root transition zone, which results in anisotropic cell expansion and root bending away from higher salt. In hydropatterning, Indole-3-acetic acid 3 (IAA3) interacts with SUMOylated-ARF7 (Auxin response factor 7) and prevents expression of Lateral organ boundaries-domain 16 (LBD16) in air-side of the root, while on wet side of the root, IAA3 cannot repress the non-SUMOylated-ARF7 thereby leading to LBD16 expression and lateral root development. In root vasculature, ABA induces expression of microRNA165/microRNA166 in endodermis, which moves into the stele to target class III Homeodomain leucine zipper protein (HD-ZIP III) mRNA in non-cell autonomous manner. The bidirectional gradient of microRNA165/6 and HD-ZIP III mRNA regulates xylem patterning under stress. Understanding the tissue specific molecular mechanisms regulating the root responses under heterogeneous and stress environments will help in designing climate-resilient crops."
Authors: Hongxue Li, Shouwen Wang, Lulu Zhai, Yuhai Cui, Guiliang Tang, Junwei Huo, Xuyan Li and Shaomin Bian.
Plant Biotechnology Journal (2023)
Abstract: "Colour change is an important event during fruit ripening in blueberry. It is well known that miR156/SPLs act as regulatory modules mediating anthocyanin biosynthesis and ethylene plays critical roles during colour change, but the intrinsic connections between the two pathways remain poorly understood. Previously, we demonstrated that blueberry VcMIR156a/VcSPL12 affects the accumulation of anthocyanins and chlorophylls in tomato and Arabidopsis. In this study, we first showed that VcMIR156a overexpression in blueberry led to enhanced anthocyanin biosynthesis, decreased chlorophyll accumulation, and, intriguingly, concomitant elevation in the expression of ethylene biosynthesis genes and the level of the ethylene precursor ACC. Conversely, VcSPL12 enhanced chlorophyll accumulation and suppressed anthocyanin biosynthesis and ACC synthesis in fruits. Moreover, the treatment with ethylene substitutes and inhibitors attenuated the effects of VcMIR156a and VcSPL12 on pigment accumulation. Protein-DNA interaction assays indicated that VcSPL12 could specifically bind to the promoters and inhibit the activities of the ethylene biosynthetic genes VcACS1 and VcACO6. Collectively, our results show that VcMIR156a/VcSPL12 alters ethylene production through targeting VcACS1 and VcACO6, therefore governing fruit colour change. Additionally, VcSPL12 may directly interact with the promoter region of the chlorophyll biosynthetic gene VcDVR, thereby activating its expression. These findings established an intrinsic connection between the miR156/SPL regulatory module and ethylene pathway."
Authors: Jutarou Fukazawa, Kazuya Mori, Hiroki Ando, Ryota Mori, Yuri Kanno, Mitsunori Seo and Yohsuke Takahashi.
Plant Physiology (2023)
Abstract: "Jasmonate (JA) and gibberellins (GAs) exert antagonistic effects on plant growth and development in response to environmental and endogenous stimuli. Although the crosstalk between JA and GA has been elucidated, the role of JA in GA biosynthesis remains unclear. Therefore, in this study, we investigated the mechanism underlying JA-mediated regulation of endogenous GA levels in Arabidopsis (Arabidopsis thaliana). Transient and electrophoretic mobility shift assays showed that transcription factor MYC2 regulates GA inactivation genes. Using transgenic plants, we further evaluated the contribution of MYC2 in regulating GA inactivation genes. JA treatment increased DELLA accumulation but did not inhibit DELLA protein degradation. Additionally, JA treatment decreased bioactive GA content, including GA4, significantly decreased the expression of GA biosynthesis genes, including ent-kaurene synthase (AtKS), GA 3β-hydroxylase (AtGA3ox1), and AtGA3ox2, and increased the expression of GA inactivation genes, including GA 2 oxidase (AtGA2ox4), AtGA2ox7, and AtGA2ox9. Conversely, JA treatment did not significantly affect gene expression in the myc2 myc3 myc4 triple mutant, demonstrating the MYC2–4-dependent effects of JA in GA biosynthesis. Additionally, JA post-transcriptionally regulated AtGA3ox1 expression. We identified microRNA miR5998 as an AtGA3ox1-associated miRNA; its overexpression inhibited plant growth by suppressing AtGA3ox1 expression. Overall, our findings indicate that JA treatment inhibits endogenous GA levels and plant growth by decreasing the expression of GA biosynthesis genes and increasing the expression of GA inactivation genes via miR5998 and MYC2 activities."
Authors: Vishnu Mishra and Ananda K. Sarkar.
Physiologia Plantarum (2023)
Abstract: "Serotonin is a well-studied pineal hormone that functions as a neurotransmitter in mammals and is found in varying amounts in diverse plant species. By modulating gene and phytohormonal crosstalk, serotonin has a significant role in plant growth and stress response, including root, shoot, flowering, morphogenesis, and adaptability responses to numerous environmental signals. Despite its prevalence and importance in plant growth and development, its molecular action, regulation, and signalling processes remain unknown. Here, we highlight the current knowledge of the role of serotonin-mediated regulation of plant growth and stress response. We focus on serotonin and its regulatory connections with phytohormonal crosstalk and address their possible functions in coordinating diverse phytohormonal responses during distinct developmental phases, correlating with melatonin. Additionally, we have also discussed the possible role of microRNAs (miRNAs) in the regulation of serotonin biosynthesis. In summary, serotonin may act as a node molecule to coordinate the balance between plant growth and stress response, which may shed light on finding its key regulatory pathways for uncovering its mysterious molecular network."
Authors: Jinghua Zhang, Xuan Zhang, Xueman Liu, Qiaofeng Pai, Yahui Wang and Xiaolin Wu.
Preprints (2023)
Abstract: "The size of seeds is particularly important for agricultural development, as it is a key trait that determines yield. It is controlled by the coordinated development of the integument, endosperm, and embryo. Large seeds are one of the important ways to improve the ultimate “sink strength” of crops, providing more nutrients for early plant growth and showing certain tolerance to abiotic stresses. There are several pathways for regulating plant seed size, including the HAIKU (IKU) pathway, ubiquitin-proteasome pathway, G (Guanosine triphosphate) protein regulatory pathway, mitogen-activated protein kinase (MAPK) pathway, transcriptional regulators pathway, phytohormone regulatory pathways including auxin, brassinosteroid (BR), gibberellin (GA), jasmonic acid (JA), cytokinin (CK), Abscisic acid (ABA), and MicroRNAs (miRNAs) regulatory pathway. This article summarized the seed size regulatory network and prospected ways to improve yield. We expect to provide valuable reference to researcher in the related field."
Authors: Leticia F. Ferigolo, Mateus H. Vicente, Joao P.O. Correa, Carlos H. Barrera-Rojas, Eder M. Silva, Geraldo F.F. Silva, Airton Carvalho Jr., Lazaro E.P. Peres, Guilherme B. Ambrosano, Gabriel R.A. Margarido, Robert Sablowski and Fabio T.S. Nogueira.
bioRxiv (2023)
Abstract: "Many developmental processes associated with fruit development take place at the floral meristem (FM). Age-regulated microRNA156 (miR156) and gibberellins (GA) interact to control flowering time, but their interplay in subsequent stages of reproductive development is poorly understood. Here, we show that GA and miR156 function in tomato FM and fruit patterning. High GA responses or overexpression of miR156 (156OE), which leads to low levels of miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL/SBP), resulted in enlarged FMs, defects in FM determinacy and fruits with increased locule number. Conversely, low GA responses reduced fruit indeterminacy and locule number, and overexpression of a miR156 resistant SlSBP15 allele (rSBP15) reduced cell number and size in the FM, as well as locule number. GA responses were partially required for the fruit defects observed in 156OE and rSBP15 plants. Transcriptome analysis and genetic interactions revealed shared and divergent functions of miR156-targeted SlSBPs, PROCERA/DELLA and the classical WUSCHEL/CLAVATA pathway, which has been previously associated with meristem size and determinacy. Our findings reveal that the miR156/SlSBP/GA regulatory module is deployed differently depending on developmental stage and create novel opportunities to genetically fine tune aspects of fruit development that have been important for tomato domestication."
Authors: Qing Sang, Lusheng Fan, Tianxiang Liu, Yongjian Qiu, Juan Du, Beixin Mo, Meng Chen and Xuemei Chen.
Nature Communications (2023)
Editor's view: Plants respond to light and temperature changes via the photoreceptor phytochrome B and the phytohormone auxin. Here the authors reveal microRNA156 as a previously uncharacterized developmental signal that gates environmentally regulated plant growth by licensing auxin sensitivity.
Abstract: MicroRNAs (miRNAs) play diverse roles in plant "development, but whether and how miRNAs participate in thermomorphogenesis remain ambiguous. Here we show that HYPONASTIC LEAVES 1 (HYL1)—a key component of miRNA biogenesis—acts downstream of the thermal regulator PHYTOCHROME INTERACTING FACTOR 4 in the temperature-dependent plasticity of hypocotyl growth in Arabidopsis. A hyl1-2 suppressor screen identified a dominant dicer-like1 allele that rescues hyl1-2’s defects in miRNA biogenesis and thermoresponsive hypocotyl elongation. Genome-wide miRNA and transcriptome analysis revealed microRNA156 (miR156) and its target SQUAMOSA PROMOTER-BINDING-PROTEIN-LIKE 9 (SPL9) to be critical regulators of thermomorphogenesis. Surprisingly, perturbation of the miR156/SPL9 module disengages seedling responsiveness to warm temperatures by impeding auxin sensitivity. Moreover, miR156-dependent auxin sensitivity also operates in the shade avoidance response at lower temperatures. Thus, these results unveil the miR156/SPL9 module as a previously uncharacterized genetic circuit that enables plant growth plasticity in response to environmental temperature and light changes."
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Authors: Muhammad Fahad, Leeza Tariq, Sajid Muhammad and Liang Wu.
Plant Communications (2024)
Abstract: "Long non-coding RNAs (lncRNAs) have emerged as integral gene expression regulators underlying plant growth, development, and adaptation. To adapt to the heterogeneous and dynamic rhizosphere, plants use interconnected regulatory mechanisms to optimally fine-tune gene expression governing interactions with soil biota, nutrient acquisition, and heavy metal tolerance. Recently, high-throughput sequencing has enabled the identification of plant lncRNAs responsive to rhizosphere biotic and abiotic cues. Here, we examine lncRNA biogenesis, classification, and mode of action, highlighting the functions of lncRNAs in mediating plant adaptation to diverse rhizosphere factors. We then discuss studies that revealed lncRNA significance and target genes during developmental plasticity and stress responses at the rhizobium interface. Thus, a comprehensive understanding of specific lncRNAs, their regulatory targets, and the intricacies of their functional interaction networks will provide crucial insights into how these transcriptomic switches fine-tune responses to shifting rhizosphere signals. As we look ahead, we foresee that single-cell dissection of cell type-specific lncRNA regulatory dynamics will enhance our understanding of precise developmental modulation mechanisms enabling plant rhizosphere adaptation. Overcoming future challenges through multi-omics and genetic approaches will better reveal the integral lncRNA roles governing plant adaptation to the belowground environment."
Authors: Ruijuan Yang, Zhenying Wu, Ying Sun, Yuchen Liu, Yuqing Hang, Min Liu, Yajun Liu, Xiaoshan Wang, Wenwen Liu and Chunxiang Fu.
The Plant Journal (2024)
Significance Statement: It is well known that excessive grass tiller number negatively impacts culm development. Suppressing CYTOKININ OXIDASE/DEHYDROGENASE4 in miR156-overexpressing background switchgrass plants reduced the negative impacts of miR156 on culm development while leaving tiller number unaffected. Finally, the double transgenic plants yielded 110% more biomass than the wild type. Thus, the trade-off between tiller number and culm development widely observed in grasses can be successfully altered through precise manipulation of the miR156-SPL2-CKX4 module."
Abstract: "Culm development in grasses can be controlled by both miR156 and cytokinin. However, the crosstalk between the miR156-SPL module and the cytokinin metabolic pathway remains largely unknown. Here, we found CYTOKININ OXIDASE/DEHYDROGENASE4 (PvCKX4) plays a negative regulatory role in culm development of the bioenergy grass Panicum virgatum (switchgrass). Overexpression of PvCKX4 in switchgrass reduced the internode diameter and length without affecting tiller number. Interestingly, we also found that PvCKX4 was always upregulated in miR156 overexpressing (miR156OE) transgenic switchgrass lines. Additionally, upregulation of either miR156 or PvCKX4 in switchgrass reduced the content of isopentenyl adenine (iP) without affecting trans-zeatin (tZ) accumulation. It is consistent with the evidence that the recombinant PvCKX4 protein exhibited much higher catalytic activity against iP than tZ in vitro. Furthermore, our results showed that miR156-targeted SPL2 bound directly to the promoter of PvCKX4 to repress its expression. Thus, alleviating the SPL2-mediated transcriptional repression of PvCKX4 through miR156 overexpression resulted in a significant increase in cytokinin degradation and impaired culm development in switchgrass. On the contrary, suppressing PvCKX4 in miR156OE transgenic plants restored iP content, internode diameter, and length to wild-type levels. Most strikingly, the double transgenic lines retained the same increased tiller numbers as the miR156OE transgenic line, which yielded more biomass than the wild type. These findings indicate that the miR156-SPL module can control culm development through transcriptional repression of PvCKX4 in switchgrass, which provides a promising target for precise design of shoot architecture to yield more biomass from grasses."
Authors: Chen Zhao, Jingjing Ma, Chen Yan, Yu Jiang, Yaohua Zhang, Yudan Lu, Ye Zhang, Suxin Yang, Xianzhong Feng and Jun Yan.
The Crop Journal (2024)
Abstract: "Drought stress limits agricultural productivity worldwide. Identifying and characterizing genetic components of drought stress-tolerance networks may improve crop resistance to drought stress. We show that the regulatory module formed by miR166 and its target gene, ATHB14-LIKE, functions in the regulation of drought tolerance in soybean (Glycine max). Drought stress represses the accumulation of miR166, leading to upregulation of its target genes. Optimal knockdown of miR166 in the stable transgenic line GmSTTM166 conferred drought tolerance without affecting yield. Expression of ABA signaling pathway genes was regulated by the miR166-mediated regulatory pathway, and ATHB14-LIKE directly activates some of these genes. There is a feedback regulation between ATHB14-LIKE and MIR166 genes, and ATHB14-LIKE inhibits MIR166 expression. These findings reveal that drought-triggered regulation of the miR166-mediated regulatory pathway increases plants drought resistance, providing new insights into drought stress regulatory network in soybean."
Authors: Shuihuan Guo, Meng Zhang, Mingxin Feng, Guipeng Liu, Laurent Torregrosa, Xiaoqing Tao, Ruihua Ren, Yulin Fang, Zhenwen Zhang, Jiangfei Meng and Tengfei Xu.
Horticulture Research (2024)
Abstract: "Anthocyanins are the primary color components of grapevine berries and wines. In cultivation practices, a moderate water deficit can promote anthocyanin accumulation in red grape skins. Our previous study showed that ABA plays a key role in this process. Herein, we identified a microRNA, vv-miR156b, that is generated in grapevine berries in response to drought stress, along with increasing anthocyanin content and biosynthetic structural gene transcripts. In contrast, the vv-miR156b short tandem target mimic (STTM) function-loss callus exhibits the opposite phenotype. Results from the in vivo and in vitro experiments revealed that the abscisic acid (ABA) signaling regulated transcription factor VvAREB2 binds directly to the ABA responsive element (ABRE) of the MIR156b promoter and activates miR156b expression. Furthermore, two miR156b downstream targets, VvSBP8 and VvSBP13, exhibited reducing grape anthocyanin content in their overexpressors and contrary resulted showed in their CRISPR-edited lines, the decrease of anthocyanin content was rescued in miR156b and SBP8/13 double overexpressors. We further demonstrated that both VvSBP8 and VvSBP13 encoding transcriptional repressors displayed sufficient ability to interact with VvMYC1 and VvMYBA1, thereby interfering with MYB–bHLH–WD (MBW) repeat transcriptional complex formation, resulting in the repression of anthocyanin biosynthesis. Our findings demonstrate a direct functional relationship between ABA signaling and the miR156-SBP-MBW complex regulatory module in driving drought-induced anthocyanin accumulation in grape berries."
Authors: Nilam N. Malankar, Kirtikumar R. Kondhare, Kishan Saha, Mohit Mantri, Anjan K Banerjee
Plant Physiology (2023)
Abstract: "Phased short-interfering RNAs (phasiRNAs) fine tune various stages of growth, development, and stress responses in plants. Potato (Solanum tuberosum) tuberization is a complex process, wherein a belowground modified stem (stolon) passes through developmental stages like swollen stolon and minituber before it matures to a potato. Previously, we identified several phasiRNA-producing loci (PHAS) from stolon-to-tuber transition stages. However, whether phasiRNAs mediate tuber development remains unknown. Here, we show that a gene encoding NB-ARC DOMAIN-CONTAINING DISEASE RESISTANCE PROTEIN (StRGA4; a PHAS locus) is targeted by Stu-microRNA482c to generate phasiRNAs. Interestingly, we observed that one of the phasiRNAs, referred as short-interfering RNA D29(-), i.e. siRD29(-), targets the gibberellin (GA) biosynthesis gene GIBBERELLIN 3-OXIDASE 3 (StGA3ox3). Since regulation of bioactive GA levels in stolons controls tuber development, we hypothesized that a gene regulatory module, Stu-miR482c-StRGA4-siRD29(-)-StGA3ox3, could govern tuber development. Through transient expression assays and small RNA sequencing, generation of siRD29(-) and its phase was confirmed in planta. Notably, the expression of StGA3ox3 was higher in swollen stolon compared to stolon, whereas siRD29(-) showed a negative association with StGA3ox3 expression. Antisense (AS) lines of StGA3ox3 produced more tubers compared to wild type. As expected, StRGA4 overexpression (OE) lines had high levels of siRD29(-) and mimicked the phenotypes of StGA3ox3-AS lines, indicating the functionality of this module in potato. In vitro tuberization assays (with or without a GA inhibitor) using StGA3ox3 antisense lines and overexpression lines of StGA3ox3 or StRGA4 revealed that StGA3ox3 controls the tuber stalk development. Taken together, our findings suggest that a phasiRNA, siRD29(-), mediates the regulation of StGA3ox3 during stolon-to-tuber transitions in potato."
Authors: Weikun Jing, Feifei Gong, Guoqin Liu, Yinglong Deng, Jiaqi Liu, Wenjing Yang, Xiaoming Sun, Yonghong Li, Junping Gao, Xiaofeng Zhou and Nan Ma.
Nature Communications (2023)
Editor's view: Expression of MIR159 is attenuated by a MYB73/TPL/HDA19 repression complex during rose petal development. Reduced MIR159 levels lead to accumulation of Cytokinin Oxidase 6, causing cytokinin clearance and subsequent arrest of cell division.
Abstract: "The size of plant lateral organs is determined by well-coordinated cell proliferation and cell expansion. Here, we report that miR159, an evolutionarily conserved microRNA, plays an essential role in regulating cell division in rose (Rosa hybrida) petals by modulating cytokinin catabolism. We uncover that Cytokinin Oxidase/Dehydrogenase6 (CKX6) is a target of miR159 in petals. Knocking down miR159 levels results in the accumulation of CKX6 transcripts and earlier cytokinin clearance, leading to a shortened cell division period and smaller petals. Conversely, knocking down CKX6 causes cytokinin accumulation and a prolonged developmental cell division period, mimicking the effects of exogenous cytokinin application. MYB73, a R2R3-type MYB transcription repressor, recruits a co-repressor (TOPLESS) and a histone deacetylase (HDA19) to form a suppression complex, which regulates MIR159 expression by modulating histone H3 lysine 9 acetylation levels at the MIR159 promoter. Our work sheds light on mechanisms for ensuring the correct timing of the exit from the cell division phase and thus organ size regulation by controlling cytokinin catabolism."
Author: Erik Stokstad.
Science (2023)
Excerpts: "Plants bred or engineered to be short can stand up better to windstorms. They could also boost yields and benefit the environment"
"Bayer’s genetic engineers have focused on a plant growth hormone called gibberellin. At first the approach looked unpromising. Decades ago researchers knocked out the genes that control early steps in gibberellin synthesis, but the result was plants that had deformed flowers and abnormal ears. Since then, scientists have adapted an approach previously used to engineer shorter versions of tomato, apple, banana, and other crops. They figured out how to suppress corn genes that code for enzymes known as gibberellin 20 oxidases, which put the biochemical finishing touches on the hormone in particular parts of the plant. This way, the levels of gibberellin can be lowered in the stalks, but not the flowers, stunting the plants’ growth without undermining their productivity. Initial attempts resulted in corn plants that were far too short to be commercially viable. But after considerable tinkering, Gillespie and her colleagues solved the problem in collaboration with the company BASF. They added DNA that encodes microRNAs, small molecules that can suppress genes. In this case the targets were two genes that regulate the creation of gibberellin mainly in the leaves and stalk, resulting in plants that were one-third shorter. To avoid shrinking the leaves as well, the researchers delivered the mutant alleles with a genetic switch from a rice virus that is most active in the stalk. Field studies in 2019 and 2020 at two locations in Illinois confirmed the manipulation did not affect the ears; they weighed the same as those from typical tall varieties, Gillespie and colleagues reported in March 2022 in the Plant Biotechnology Journal. This successful change in stature by interfering with gibberellin was “the first of its kind in corn,” says Guri Johal, a corn geneticist at Purdue who has discovered a mutation, called D16, with a similar effect."
Authors: Kejing Fan, Zhili Wang, Ching-Ching Sze, Yongchao Niu, Fuk-Ling Wong, Man-Wah Li and Hon-Ming Lam.
New Phytologist (2023)
Abstract: "MicroRNAs (miRNAs) are important regulators of plant biological processes, including soybean nodulation. One miRNA, miR4407, was identified in soybean roots and nodules. However, the function of miR4407 in soybean is still unknown. MiR4407, unique to soybean, positively regulates lateral root emergence and root structures and represses a root-specific ISOPENTENYLTRANSFERASE (GmIPT3). By altering the expression of miR4407 and GmIPT3, we investigated the role of miR4407 in lateral root and nodule development. Both miR4407 and GmIPT3 are expressed in the inner root cortex and nodule primordia. Upon rhizobial inoculation, miR4407 was downregulated while GmIPT3 was upregulated. Overexpressing miR4407 reduced the number of nodules in transgenic soybean hairy roots while overexpressing the wild-type GmIPT3 or a miR4407-resistant GmIPT3 mutant (mGmIPT3) significantly increased the nodule number. The mechanism of miR4407 and GmIPT3 functions was also linked to autoregulation of nodulation (AON), where miR4407 overexpression repressed miR172c and activated its target, GmNNC1, turning on AON. Exogenous CK mimicked the effects of GmIPT3 overexpression on miR172c, supporting the notion that GmIPT3 regulates nodulation by enhancing root-derived CK. Overall, our data revealed a new miRNA-mediated regulatory mechanism of nodulation in soybean. MiR4407 showed a dual role in lateral root and nodule development."
Authors: Daria Scintu, Emanuele Scacchi, Francesca Cazzaniga, Federico Vinciarelli, Mirko De Vivo, Margaryta Shtin, Noemi Svolacchia, Gaia Bertolotti, Simon Joseph Unterholzener, Marta Del Bianco, Marja Timmermans, Riccardo Di Mambro, Paola Vittorioso, Sabrina Sabatini, Paolo Costantino and Raffaele Dello Ioio
Communications Biology (2023)
Editor's view: Genetic, molecular, and computational analyses reveal that salt stress alters root apical meristem size through miR165/166-mediated regulation of cytokinin levels via the PHB-IPT7 pathway.
Abstract: "In plants, developmental plasticity allows for the modulation of organ growth in response to environmental cues. Being in contact with soil, roots are the first organ that responds to various types of soil abiotic stress such as high salt concentration. In the root, developmental plasticity relies on changes in the activity of the apical meristem, the region at the tip of the root where a set of self-renewing undifferentiated stem cells sustain growth. Here, we show that salt stress promotes differentiation of root meristem cells via reducing the dosage of the microRNAs miR165 and 166. By means of genetic, molecular and computational analysis, we show that the levels of miR165 and 166 respond to high salt concentration, and that miR165 and 166-dependent PHABULOSA (PHB) modulation is central to the response of root growth to this stress. Specifically, we show that salt-dependent reduction of miR165 and 166 causes a rapid increase in PHB expression and, hence, production of the root meristem pro-differentiation hormone cytokinin. Our data provide direct evidence for how the miRNA-dependent modulation of transcription factor dosage mediates plastic development in plants"
Authors: Jinghua Zhang, Xuan Zhang, Xueman Liu, Qiaofeng Pai, Yahui Wang and Xiaolin Wu.
International Journal of Molecular Sciences (2023)
Abstract: "The size of seeds is particularly important for agricultural development, as it is a key trait that determines yield. It is controlled by the coordinated development of the integument, endosperm, and embryo. Large seeds are an important way of improving the ultimate “sink strength” of crops, providing more nutrients for early plant growth and showing certain tolerance to abiotic stresses. There are several pathways for regulating plant seed size, including the HAIKU (IKU) pathway, ubiquitin–proteasome pathway, G (Guanosine triphosphate) protein regulatory pathway, mitogen-activated protein kinase (MAPK) pathway, transcriptional regulators pathway, and phytohormone regulatory pathways including the auxin, brassinosteroid (BR), gibberellin (GA), jasmonic acid (JA), cytokinin (CK), Abscisic acid (ABA), and microRNA (miRNA) regulatory pathways. This article summarizes the seed size regulatory network and prospective ways of improving yield. We expect that it will provide a valuable reference to researchers in related fields."
Authors: Pan Luo and Dong-Wei Di.
International Journal of Molecular Sciences (2023)
Abstract: "The indole-3-pyruvic acid (IPA) pathway is the main auxin biosynthesis pathway in the plant kingdom. Local control of auxin biosynthesis through this pathway regulates plant growth and development and the responses to biotic and abiotic stresses. During the past decades, genetic, physiological, biochemical, and molecular studies have greatly advanced our understanding of tryptophan-dependent auxin biosynthesis. The IPA pathway includes two steps: Trp is converted to IPA by TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS/TRYPTOPHAN AMINOTRANSFERASE RELATED PROTEINs (TAA1/TARs), and then IPA is converted to IAA by the flavin monooxygenases (YUCCAs). The IPA pathway is regulated at multiple levels, including transcriptional and post-transcriptional regulation, protein modification, and feedback regulation, resulting in changes in gene transcription, enzyme activity and protein localization. Ongoing research indicates that tissue-specific DNA methylation and miRNA-directed regulation of transcription factors may also play key roles in the precise regulation of IPA-dependent auxin biosynthesis in plants. This review will mainly summarize the regulatory mechanisms of the IPA pathway and address the many unresolved questions regarding this auxin biosynthesis pathway in plants."
Authors: Xiaomin Liu, Tengteng Gao, Changhai Liu, Ke Mao, Xiaoqing Gong, Chao Li and Fengwang Ma.
Plant Physiology (2023)
Abstract: "Drought is a common stress in agricultural production. Thus, it is imperative to understand how fruit crops respond to drought and to develop drought-tolerant varieties. This paper provides an overview of the effects of drought on the vegetative and reproductive growth of fruits. We summarize the empirical studies that have assessed the physiological and molecular mechanisms of the drought response in fruit crops. This review focuses on the roles of calcium (Ca2+) signaling, abscisic acid (ABA), reactive oxygen species (ROS) signaling, and protein phosphorylation underlying the early drought response in plants. We review the resulting downstream ABA-dependent and ABA-independent transcriptional regulation in fruit crops under drought stress. Moreover, we highlight the positive and negative regulatory mechanisms of microRNAs in the drought response of fruit crops. Lastly, strategies (including breeding and agricultural practices) to improve the drought resistance of fruit crops are outlined."
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