cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26723044.v1
title: MAPK3-MYB36-ARF1 module regulates the tanshinone formation in <i>Salvia miltiorrhiza</i>

description: <i>Salvia miltiorrhiza</i>, known as Danshen, is a traditional Chinese medicinal plant with significant cardiovascular benefits, attributed to its secondary metabolites, particularly tanshinones. Despite their medicinal value, tanshinones occur in low natural abundance, necessitating research to increase their content. This study explores the role of the ARF transcription factor (SmARF1) in tanshinone accumulation in Danshen. Overexpressing <i>SmARF1</i> in hairy roots significantly increased tanshinone levels. EMSA and Dual-LUC assays revealed that SmMYB36, a transcription factor interacting with SmMAPK3, binds to and regulates the <i>SmARF1</i> promoter. SmMYB36 alone inhibited the expression of <i>SmARF1</i> gene, while its interaction with SmMAPK3 enhanced <i>SmARF1</i> promoter activity. This MAPK3-MYB36-ARF1 module elucidates a complex regulatory mechanism for tanshinone biosynthesis, offering insights for targeted enhancement of tanshinone content through advanced biotechnological approaches.
DOI: 10.6084/m9.figshare.25425898
title: Distinct interactions of ericoid mycorrhizae and plant growth-promoting bacteria: impacts on blueberry growth and heat resilience

description: Blueberries confront substantial challenges from climate change, such as rising temperatures and extreme heat, necessitating urgent solutions to ensure productivity. We hypothesized that ericoid mycorrhizal fungi (ErM) and plant growth-promoting bacteria (PGPB) would establish symbiotic relationships and increase heat stress tolerance in blueberries. A growth chamber study was designed with low (25/20°C) and high temperature (35/30°C) conditions with micropropagated blueberry plantlets inoculated with ErM, PGPB, and both. Gas exchange and chlorophyll fluorescence properties of the leaves were monitored throughout the growth. At harvest, biochemical assays and biomass analysis were performed to evaluate potential oxidative stress induced by elevated temperatures. ErM application boosted root biomass under 25/20°C conditions but did not impact photosynthetic efficiency. In contrast, PGPB demonstrated a dual role: enhancing photosynthetic capacity and reducing stomatal conductance notably under 35/30°C conditions. Moreover, PGPB showcased conflicting effects, reducing oxidative damage under 25/20°C conditions while intensifying it during 47°C heat shock. A significant highlight lies in the opposing effects of ErM and PGPB on root growth and stomatal conductance, signifying their reciprocal influence on blueberry plant behavior, which may lead to increased water uptake or reduced water use. Understanding these complex interactions holds promise for refining sustainable strategies to overcome climate challenges.
DOI: 10.6084/m9.figshare.25872182
title: HDACs MADS-domain protein interaction: a case study of HDA15 and XAL1 in <i>Arabidopsis thaliana</i>

description: Cellular behavior, cell differentiation and ontogenetic development in eukaryotes result from complex interactions between epigenetic and classic molecular genetic mechanisms, with many of these interactions still to be elucidated. Histone deacetylase enzymes (HDACs) promote the interaction of histones with DNA by compacting the nucleosome, thus causing transcriptional repression. MADS-domain transcription factors are highly conserved in eukaryotes and participate in controlling diverse developmental processes in animals and plants, as well as regulating stress responses in plants. In this work, we focused on finding out putative interactions of <i>Arabidopsis thaliana</i> HDACs and MADS-domain proteins using an evolutionary perspective combined with bioinformatics analyses and testing the more promising predicted interactions through classic molecular biology tools. Through bioinformatic analyses, we found similarities between HDACs proteins from different organisms, which allowed us to predict a putative protein-protein interaction between the <i>Arabidopsis thaliana</i> deacetylase HDA15 and the MADS-domain protein XAANTAL1 (XAL1). The results of two-hybrid and Bimolecular Fluorescence Complementation analysis demonstrated <i>in vitro</i> and <i>in vivo</i> HDA15-XAL1 interaction in the nucleus. Likely, this interaction might regulate developmental processes in plants as is the case for this type of interaction in animals.
DOI: 10.6084/m9.figshare.25872182.v1
title: HDACs MADS-domain protein interaction: a case study of HDA15 and XAL1 in <i>Arabidopsis thaliana</i>

description: Cellular behavior, cell differentiation and ontogenetic development in eukaryotes result from complex interactions between epigenetic and classic molecular genetic mechanisms, with many of these interactions still to be elucidated. Histone deacetylase enzymes (HDACs) promote the interaction of histones with DNA by compacting the nucleosome, thus causing transcriptional repression. MADS-domain transcription factors are highly conserved in eukaryotes and participate in controlling diverse developmental processes in animals and plants, as well as regulating stress responses in plants. In this work, we focused on finding out putative interactions of <i>Arabidopsis thaliana</i> HDACs and MADS-domain proteins using an evolutionary perspective combined with bioinformatics analyses and testing the more promising predicted interactions through classic molecular biology tools. Through bioinformatic analyses, we found similarities between HDACs proteins from different organisms, which allowed us to predict a putative protein-protein interaction between the <i>Arabidopsis thaliana</i> deacetylase HDA15 and the MADS-domain protein XAANTAL1 (XAL1). The results of two-hybrid and Bimolecular Fluorescence Complementation analysis demonstrated <i>in vitro</i> and <i>in vivo</i> HDA15-XAL1 interaction in the nucleus. Likely, this interaction might regulate developmental processes in plants as is the case for this type of interaction in animals.
DOI: 10.6084/m9.figshare.25904873
title: syn-tasiRnas targeting the coat protein of potato virus Y confer antiviral resistance in <i>Nicotiana benthamiana</i>

description: Trans-acting small interfering RNAs (tasiRNAs) are 21-nt phased (phased siRNAs) resulting from successive DCL-catalyzed processing from the end of a double-stranded RNA substrate originating from the RDR of an AGO-catalyzed cleaved RNA at a micro RNA target site. Plant tasiRNAs have been synthesized to produce synthetic tasiRNAs (syn-tasiRNAs) targeting viral RNAs that confer viral resistance. In this study, we engineered syn-tasiRNAs to target potato virus Y (PVY) infection by replacing five native siRNAs of TAS1c with 210-bp fragments from the coat protein (CP) region of the PVY genome. The results showed that the transient expression of syn-tasiR-CPpvy2 in Nicotiana benthamiana (N. benthamiana) plants conferred antiviral resistance, supported by the absence of PVY infection symptoms and viral accumulation. This indicated that syn-tasiR-CPpvy2 successfully targeted and silenced the PVY CP gene, effectively inhibiting viral infection. syn-tasiR-CPpvy1 displayed attenuated symptoms and decreased viral accumulation in these plants However, severe symptoms of PVY infection and a similar amount of viral accumulation as the control were observed in plants expressing syn-tasiR-CPpvy3. syn-tasiR-CPpvy/pvx, which targets both PVY and potato virus X (PVX), was engineered using a single precursor. After the transient expression of syn-tasiR-CPpvy/pvx3 and syn-tasiR-CPpvy/pvx5 in N. benthamiana, the plants were resistant to both PVY and PVX. These results suggested that engineered syn-tasiRNAs could not only specifically induce antiviral resistance against one target virus but could also be designed for multi-targeted silencing of different viruses, thereby preventing complex virus infection in plants.
DOI: 10.6084/m9.figshare.25904873.v1
title: syn-tasiRnas targeting the coat protein of potato virus Y confer antiviral resistance in <i>Nicotiana benthamiana</i>

description: Trans-acting small interfering RNAs (tasiRNAs) are 21-nt phased (phased siRNAs) resulting from successive DCL-catalyzed processing from the end of a double-stranded RNA substrate originating from the RDR of an AGO-catalyzed cleaved RNA at a micro RNA target site. Plant tasiRNAs have been synthesized to produce synthetic tasiRNAs (syn-tasiRNAs) targeting viral RNAs that confer viral resistance. In this study, we engineered syn-tasiRNAs to target potato virus Y (PVY) infection by replacing five native siRNAs of TAS1c with 210-bp fragments from the coat protein (CP) region of the PVY genome. The results showed that the transient expression of syn-tasiR-CPpvy2 in Nicotiana benthamiana (N. benthamiana) plants conferred antiviral resistance, supported by the absence of PVY infection symptoms and viral accumulation. This indicated that syn-tasiR-CPpvy2 successfully targeted and silenced the PVY CP gene, effectively inhibiting viral infection. syn-tasiR-CPpvy1 displayed attenuated symptoms and decreased viral accumulation in these plants However, severe symptoms of PVY infection and a similar amount of viral accumulation as the control were observed in plants expressing syn-tasiR-CPpvy3. syn-tasiR-CPpvy/pvx, which targets both PVY and potato virus X (PVX), was engineered using a single precursor. After the transient expression of syn-tasiR-CPpvy/pvx3 and syn-tasiR-CPpvy/pvx5 in N. benthamiana, the plants were resistant to both PVY and PVX. These results suggested that engineered syn-tasiRNAs could not only specifically induce antiviral resistance against one target virus but could also be designed for multi-targeted silencing of different viruses, thereby preventing complex virus infection in plants.
DOI: 10.6084/m9.figshare.25425898.v1
title: Distinct interactions of ericoid mycorrhizae and plant growth-promoting bacteria: impacts on blueberry growth and heat resilience

description: Blueberries confront substantial challenges from climate change, such as rising temperatures and extreme heat, necessitating urgent solutions to ensure productivity. We hypothesized that ericoid mycorrhizal fungi (ErM) and plant growth-promoting bacteria (PGPB) would establish symbiotic relationships and increase heat stress tolerance in blueberries. A growth chamber study was designed with low (25/20°C) and high temperature (35/30°C) conditions with micropropagated blueberry plantlets inoculated with ErM, PGPB, and both. Gas exchange and chlorophyll fluorescence properties of the leaves were monitored throughout the growth. At harvest, biochemical assays and biomass analysis were performed to evaluate potential oxidative stress induced by elevated temperatures. ErM application boosted root biomass under 25/20°C conditions but did not impact photosynthetic efficiency. In contrast, PGPB demonstrated a dual role: enhancing photosynthetic capacity and reducing stomatal conductance notably under 35/30°C conditions. Moreover, PGPB showcased conflicting effects, reducing oxidative damage under 25/20°C conditions while intensifying it during 47°C heat shock. A significant highlight lies in the opposing effects of ErM and PGPB on root growth and stomatal conductance, signifying their reciprocal influence on blueberry plant behavior, which may lead to increased water uptake or reduced water use. Understanding these complex interactions holds promise for refining sustainable strategies to overcome climate challenges.
DOI: 10.6084/m9.figshare.25574533
title: Unveiling kiwifruit TCP genes: evolution, functions, and expression insights

description: The <i>TEOSINTE-BRANCHED1/CYCLOIDEA/PROLEFERATING-CELL-FACTORS</i> (TCP) gene family is a plant-specific transcriptional factor family involved in leaf morphogenesis and senescence, lateral branching, hormone crosstalk, and stress responses. To date, a systematic study on the identification and characterization of the <i>TCP</i> gene family in kiwifruit has not been reported. Additionally, the function of kiwifruit TCPs in regulating kiwifruit responses to the ethylene treatment and bacterial canker disease pathogen (<i>Pseudomonas syringae</i> pv. <i>actinidiae</i>, Psa) has not been investigated. Here, we identified 40 and 26 <i>TCP</i> genes in <i>Actinidia chinensis</i> (Ac) and <i>A. eriantha</i> (Ae) genomes, respectively. The synteny analysis of <i>AcTCPs</i> illustrated that whole-genome duplication accounted for the expansion of the <i>TCP</i> family in Ac. Phylogenetic, conserved domain, and selection pressure analysis indicated that <i>TCP</i> family genes in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in <i>TCP</i> gene number and distribution. Our results also suggested that protein structure and <i>cis</i>-element architecture in promoter regions of TCP genes have driven the function divergence of duplicated gene pairs. Three and four <i>AcTCP</i> genes significantly affected kiwifruit responses to the ethylene treatment and Psa invasion, respectively. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit <i>TCPs</i>.
DOI: 10.6084/m9.figshare.25721978.v1
title: Research on the function of <i>CsMYB36</i> based on an effective hair root transformation system

description: The hairy root induction system was used to efficiently investigate gene expression and function in plant root. Cucumber is a significant vegetable crop worldwide, with shallow roots, few lateral roots, and weak root systems, resulting in low nutrient absorption and utilization efficiency. Identifying essential genes related to root development and nutrient absorption is an effective way to improve the growth and development of cucumbers. However, genetic mechanisms underlying cucumber root development have not been explored. Here, we report a novel, rapid, effective hairy root transformation system. Compared to the in vitro cotyledon transformation method, this method shortened the time needed to obtain transgenic roots by 13 days. Furthermore, we combined this root transformation method with CRISPR/Cas9 technology and validated our system by exploring the expression and function of <i>CsMYB36</i>, a pivotal gene associated with root development and nutrient uptake. The hairy root transformation system established in this study provides a powerful method for rapidly identifying essential genes related to root development in cucumber and other horticultural crop species. This advancement holds promise for expediting research on root biology and molecular breeding strategies, contributing to the broader understanding and improvements crop growth and development.
DOI: 10.6084/m9.figshare.26075971
title: Proteome-wide analysis reveals G protein-coupled receptor-like proteins in rice (<i>Oryza sativa</i>)

description: G protein-coupled receptors (GPCRs) constitute the largest family of transmembrane proteins in metazoans that mediate the regulation of various physiological responses to discrete ligands through heterotrimeric G protein subunits. The existence of GPCRs in plant is contentious, but their comparable crucial role in various signaling pathways necessitates the identification of novel remote GPCR-like proteins that essentially interact with the plant G protein α subunit and facilitate the transduction of various stimuli. In this study, we identified three putative GPCR-like proteins (OsGPCRLPs) (LOC_Os06g09930.1, LOC_Os04g36630.1, and LOC_Os01g54784.1) in the rice proteome using a stringent bioinformatics workflow. The identified OsGPCRLPs exhibited a canonical GPCR ‘type I’ 7TM topology, patterns, and biologically significant sites for membrane anchorage and desensitization. Cluster-based interactome mapping revealed that the identified proteins interact with the G protein α subunit which is a characteristic feature of GPCRs. Computational results showing the interaction of identified GPCR-like proteins with G protein α subunit and its further validation by the membrane yeast-two-hybrid assay strongly suggest the presence of GPCR-like 7TM proteins in the rice proteome. The absence of a regulator of G protein signaling (RGS) box in the C- terminal domain, and the presence of signature motifs of canonical GPCR in the identified OsGPCRLPs strongly suggest that the rice proteome contains GPCR-like proteins that might be involved in signal transduction.
DOI: 10.6084/m9.figshare.26075971.v1
title: Proteome-wide analysis reveals G protein-coupled receptor-like proteins in rice (<i>Oryza sativa</i>)

description: G protein-coupled receptors (GPCRs) constitute the largest family of transmembrane proteins in metazoans that mediate the regulation of various physiological responses to discrete ligands through heterotrimeric G protein subunits. The existence of GPCRs in plant is contentious, but their comparable crucial role in various signaling pathways necessitates the identification of novel remote GPCR-like proteins that essentially interact with the plant G protein α subunit and facilitate the transduction of various stimuli. In this study, we identified three putative GPCR-like proteins (OsGPCRLPs) (LOC_Os06g09930.1, LOC_Os04g36630.1, and LOC_Os01g54784.1) in the rice proteome using a stringent bioinformatics workflow. The identified OsGPCRLPs exhibited a canonical GPCR ‘type I’ 7TM topology, patterns, and biologically significant sites for membrane anchorage and desensitization. Cluster-based interactome mapping revealed that the identified proteins interact with the G protein α subunit which is a characteristic feature of GPCRs. Computational results showing the interaction of identified GPCR-like proteins with G protein α subunit and its further validation by the membrane yeast-two-hybrid assay strongly suggest the presence of GPCR-like 7TM proteins in the rice proteome. The absence of a regulator of G protein signaling (RGS) box in the C- terminal domain, and the presence of signature motifs of canonical GPCR in the identified OsGPCRLPs strongly suggest that the rice proteome contains GPCR-like proteins that might be involved in signal transduction.
DOI: 10.6084/m9.figshare.25574533.v1
title: Unveiling kiwifruit TCP genes: evolution, functions, and expression insights

description: The <i>TEOSINTE-BRANCHED1/CYCLOIDEA/PROLEFERATING-CELL-FACTORS</i> (TCP) gene family is a plant-specific transcriptional factor family involved in leaf morphogenesis and senescence, lateral branching, hormone crosstalk, and stress responses. To date, a systematic study on the identification and characterization of the <i>TCP</i> gene family in kiwifruit has not been reported. Additionally, the function of kiwifruit TCPs in regulating kiwifruit responses to the ethylene treatment and bacterial canker disease pathogen (<i>Pseudomonas syringae</i> pv. <i>actinidiae</i>, Psa) has not been investigated. Here, we identified 40 and 26 <i>TCP</i> genes in <i>Actinidia chinensis</i> (Ac) and <i>A. eriantha</i> (Ae) genomes, respectively. The synteny analysis of <i>AcTCPs</i> illustrated that whole-genome duplication accounted for the expansion of the <i>TCP</i> family in Ac. Phylogenetic, conserved domain, and selection pressure analysis indicated that <i>TCP</i> family genes in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in <i>TCP</i> gene number and distribution. Our results also suggested that protein structure and <i>cis</i>-element architecture in promoter regions of TCP genes have driven the function divergence of duplicated gene pairs. Three and four <i>AcTCP</i> genes significantly affected kiwifruit responses to the ethylene treatment and Psa invasion, respectively. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit <i>TCPs</i>.
DOI: 10.6084/m9.figshare.25721978
title: Research on the function of <i>CsMYB36</i> based on an effective hair root transformation system

description: The hairy root induction system was used to efficiently investigate gene expression and function in plant root. Cucumber is a significant vegetable crop worldwide, with shallow roots, few lateral roots, and weak root systems, resulting in low nutrient absorption and utilization efficiency. Identifying essential genes related to root development and nutrient absorption is an effective way to improve the growth and development of cucumbers. However, genetic mechanisms underlying cucumber root development have not been explored. Here, we report a novel, rapid, effective hairy root transformation system. Compared to the in vitro cotyledon transformation method, this method shortened the time needed to obtain transgenic roots by 13 days. Furthermore, we combined this root transformation method with CRISPR/Cas9 technology and validated our system by exploring the expression and function of <i>CsMYB36</i>, a pivotal gene associated with root development and nutrient uptake. The hairy root transformation system established in this study provides a powerful method for rapidly identifying essential genes related to root development in cucumber and other horticultural crop species. This advancement holds promise for expediting research on root biology and molecular breeding strategies, contributing to the broader understanding and improvements crop growth and development.
DOI: 10.6084/m9.figshare.25752510
title: Investigation of <i>Arabidopsis</i> root skototropism with different distance settings

description: Plants can activate protective and defense mechanisms under biotic and abiotic stresses. Their roots naturally grow in the soil, but when they encounter sunlight in the top-soil layers, they may move away from the light source to seek darkness. Here we investigate the skototropic behavior of roots, which promotes their fitness and survival. Glutamate-like receptors (GLRs) of plants play roles in sensing and responding to signals, but their role in root skototropism is not yet understood. Light-induced tropisms are known to be affected by auxin distribution, mainly determined by auxin efflux proteins (PIN proteins) at the root tip. However, the role of PIN proteins in root skototropism has not been investigated yet. To better understand root skototropism and its connection to the distance between roots and light, we established five distance settings between seedlings and darkness to investigate the variations in root bending tendencies. We compared differences in root skototropic behavior across different expression lines of <i>Arabidopsis thaliana</i> seedlings (<i>atglr3.7 ko, AtGLR3.7 OE</i>, and <i>pin2 knockout</i>) to comprehend their functions. Our research shows that as the distance between roots and darkness increases, the root’s positive skototropism noticeably weakens. Our findings highlight the involvement of GLR3.7 and PIN2 in root skototropism.