cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21905717
title: Localization of <i>Arabidopsis</i> Glucan Synthase-Like 5, 8, and 12 to plasmodesmata and the GSL8-dependent role of PDLP5 in regulating plasmodesmal permeability

description: Cell-to-cell communication via membranous channels called plasmodesmata (PD) plays critical roles during plant development and in response to biotic and abiotic stresses. Several enzymes and receptor-like proteins (RLPs), including <i>Arabidopsis thaliana</i> glucan synthase-likes (GSLs), also known as callose synthases (CALSs), and PD-located proteins (PDLPs), have been implicated in plasmodesmal permeability regulation and intercellular communication. Localization of PDLPs to punctate structures at the cell periphery and their receptor-like identity have raised the hypothesis that PDLPs are involved in the regulation of symplastic trafficking during plant development and in response to endogenous and exogenous signals. Indeed, it was shown that PDLP5 could limit plasmodesmal permeability through inducing an increase in callose accumulation at PD. However, mechanistically, how this is achieved remains to be elucidated. To address this key issue in understanding the regulation of PD, physical and functional interactions between PDLPs and GSLs (using the PDLP5–GSL8/CALS10 pair as a model) were investigated. Our results show that GSL8/CALS10 plays essential roles and is required for the function and plasmodesmal localization of PDLP5. Furthermore, it was demonstrated that the localization of PDLP5 to PD and its function in inducing callose deposition are GSL8-dependent. Importantly, our transgenic study shows that three key members of the GSL family, i.e., GSL5/CALS12, GSL8/CALS10, and GSL12/CALS3, localize to PD and co-localize with PDLP5, suggesting that GSL8/CALS10 might not be the only callose synthase with the determining role in PD regulation. These findings, together with our previous observation showing the direct interaction of GSL8/CALS10 with PDLP5, indicate the pivotal role of the GSL8/CALS10-PDLP5 interplay in regulating PD permeability. Future work is needed to investigate whether the PDLP5 functionality and localization are also disrupted in <i>gsl5</i> and <i>gsl12</i>, or it is just <i>gsl8</i>-specific.
DOI: 10.6084/m9.figshare.21905717.v1
title: Localization of <i>Arabidopsis</i> Glucan Synthase-Like 5, 8, and 12 to plasmodesmata and the GSL8-dependent role of PDLP5 in regulating plasmodesmal permeability

description: Cell-to-cell communication via membranous channels called plasmodesmata (PD) plays critical roles during plant development and in response to biotic and abiotic stresses. Several enzymes and receptor-like proteins (RLPs), including <i>Arabidopsis thaliana</i> glucan synthase-likes (GSLs), also known as callose synthases (CALSs), and PD-located proteins (PDLPs), have been implicated in plasmodesmal permeability regulation and intercellular communication. Localization of PDLPs to punctate structures at the cell periphery and their receptor-like identity have raised the hypothesis that PDLPs are involved in the regulation of symplastic trafficking during plant development and in response to endogenous and exogenous signals. Indeed, it was shown that PDLP5 could limit plasmodesmal permeability through inducing an increase in callose accumulation at PD. However, mechanistically, how this is achieved remains to be elucidated. To address this key issue in understanding the regulation of PD, physical and functional interactions between PDLPs and GSLs (using the PDLP5–GSL8/CALS10 pair as a model) were investigated. Our results show that GSL8/CALS10 plays essential roles and is required for the function and plasmodesmal localization of PDLP5. Furthermore, it was demonstrated that the localization of PDLP5 to PD and its function in inducing callose deposition are GSL8-dependent. Importantly, our transgenic study shows that three key members of the GSL family, i.e., GSL5/CALS12, GSL8/CALS10, and GSL12/CALS3, localize to PD and co-localize with PDLP5, suggesting that GSL8/CALS10 might not be the only callose synthase with the determining role in PD regulation. These findings, together with our previous observation showing the direct interaction of GSL8/CALS10 with PDLP5, indicate the pivotal role of the GSL8/CALS10-PDLP5 interplay in regulating PD permeability. Future work is needed to investigate whether the PDLP5 functionality and localization are also disrupted in <i>gsl5</i> and <i>gsl12</i>, or it is just <i>gsl8</i>-specific.
DOI: 10.6084/m9.figshare.23921952
title: Comparative analysis of sorghum (C4) and rice (C3) plant headspace volatiles induced by artificial herbivory

description: Acute stress responses include release of defensive volatiles from herbivore-attacked plants. Here we used two closely related monocot species, rice as a representative C3 plant, and sorghum as a representative C4 plant, and compared their basal and stress-induced headspace volatile organic compounds (VOCs). Although both plants emitted similar types of constitutive and induced VOCs, in agreement with the close phylogenetic relationship of the species, several mono- and sesquiterpenes have been significantly less abundant in headspace of sorghum relative to rice. Furthermore, in spite of generally lower VOC levels, some compounds, such as the green leaf volatile (<i>Z</i>)-3-hexenyl acetate and homoterpene DMNT, remained relatively high in the sorghum headspace, suggesting that a separate mechanism for dispersal of these compounds may have evolved in this plant. Finally, a variable amount of several VOCs among three sorghum cultivars of different geographical origins suggested that release of VOCs could be used as a valuable resource for the increase of sorghum resistance against herbivores. This paper shows how genetically related plants with similar volatile toolboxes define their own species identity in the ecological space.
DOI: 10.6084/m9.figshare.23921952.v1
title: Comparative analysis of sorghum (C4) and rice (C3) plant headspace volatiles induced by artificial herbivory

description: Acute stress responses include release of defensive volatiles from herbivore-attacked plants. Here we used two closely related monocot species, rice as a representative C3 plant, and sorghum as a representative C4 plant, and compared their basal and stress-induced headspace volatile organic compounds (VOCs). Although both plants emitted similar types of constitutive and induced VOCs, in agreement with the close phylogenetic relationship of the species, several mono- and sesquiterpenes have been significantly less abundant in headspace of sorghum relative to rice. Furthermore, in spite of generally lower VOC levels, some compounds, such as the green leaf volatile (<i>Z</i>)-3-hexenyl acetate and homoterpene DMNT, remained relatively high in the sorghum headspace, suggesting that a separate mechanism for dispersal of these compounds may have evolved in this plant. Finally, a variable amount of several VOCs among three sorghum cultivars of different geographical origins suggested that release of VOCs could be used as a valuable resource for the increase of sorghum resistance against herbivores. This paper shows how genetically related plants with similar volatile toolboxes define their own species identity in the ecological space.
DOI: 10.6084/m9.figshare.24439019
title: An <i>Arabidopsis</i> mutant line lacking the mitochondrial calcium transport regulator MICU shows an altered metabolite profile

description: Plant metabolism is constantly changing and requires input signals for efficient regulation. The mitochondrial calcium uniporter (MCU) couples organellar and cytoplasmic calcium oscillations leading to oxidative metabolism regulation in a vast array of species. In <i>Arabidopsis thaliana</i>, genetic deletion of AtMICU leads to altered mitochondrial calcium handling and ultrastructure. Here we aimed to further assess the consequences upon genetic deletion of AtMICU. Our results confirm that AtMICU safeguards intracellular calcium transport associated with carbohydrate, amino acid, and phytol metabolism modifications. The implications of such alterations are discussed.
DOI: 10.6084/m9.figshare.24545778
title: Comparative transcriptomic and weighted gene co-expression network analysis to identify the core genes in the cultivars of <i>Musa acuminata</i> under both infected and chemical perturbated conditions

description: Banana is a high nutrient crop, which ranks fourth in terms of gross value production. Fusarium wilt of banana, caused by <i>Fusarium oxysporum f. sp. cubense</i> tropical race 4 (FocTR4), is considered the most destructive disease leading to the complete loss of production of the Cavendish cultivars Berangan, Brazilian and Williams, which are vulnerable to the infection of FocTR4. However, the treatment with benzothiadiazole, a synthetic salicylic analog, is aimed to induce resistance in plants. Thus, the treatments pertaining to the banana plants subjected to the Foc infection within the chosen cultivars were compared with chemically treated samples obtained at different time intervals for a short duration (0–4 days). The integrated omics analyses considering the parameters of WGCNA, functional annotation, and protein–protein interactions revealed that many pathways have been negatively influenced in Cavendish bananas under FocTR4 infections and the number of genes influenced also increased over time in Williams cultivar. Furthermore, elevation in immune response and resistance genes were also observed in the roots of the Cavendish banana.
DOI: 10.6084/m9.figshare.24545778.v1
title: Comparative transcriptomic and weighted gene co-expression network analysis to identify the core genes in the cultivars of <i>Musa acuminata</i> under both infected and chemical perturbated conditions

description: Banana is a high nutrient crop, which ranks fourth in terms of gross value production. Fusarium wilt of banana, caused by <i>Fusarium oxysporum f. sp. cubense</i> tropical race 4 (FocTR4), is considered the most destructive disease leading to the complete loss of production of the Cavendish cultivars Berangan, Brazilian and Williams, which are vulnerable to the infection of FocTR4. However, the treatment with benzothiadiazole, a synthetic salicylic analog, is aimed to induce resistance in plants. Thus, the treatments pertaining to the banana plants subjected to the Foc infection within the chosen cultivars were compared with chemically treated samples obtained at different time intervals for a short duration (0–4 days). The integrated omics analyses considering the parameters of WGCNA, functional annotation, and protein–protein interactions revealed that many pathways have been negatively influenced in Cavendish bananas under FocTR4 infections and the number of genes influenced also increased over time in Williams cultivar. Furthermore, elevation in immune response and resistance genes were also observed in the roots of the Cavendish banana.
DOI: 10.6084/m9.figshare.24886565
title: Systematic analysis of the thioredoxin gene family in <i> Citrus sinensis</i>: identification, phylogenetic analysis, and gene expression patterns

description: Thioredoxin (TRX) proteins play essential roles in reactive oxygen species scavenging in plants. We executed an exhaustive analysis of the TRX gene family in <i>Citrus sinensis</i> (<i>CsTRXs</i>), encompassing identification, phylogenetic analysis, detection of conserved motifs and domains, gene structure, cis-acting elements, gene expression trends, and subcellular localization analysis. Our findings established that a total of 22 <i>CsTRXs</i> with thioredoxin domains were identified in the genome of <i>C. sinensis</i>. Phylogenetic analysis indicated that CsTRXs were divided into six subclusters. Conserved motifs analysis of CsTRXs indicated a wide range of conserved motifs. A significant number of cis-acting elements associated with both abiotic and biotic stress responses, inclusive of numerous phytohormone-related elements, were detected in the promoter regions of <i>CsTRXs</i>. The expression levels of <i>CsTRXs</i> including <i>CsTRXf1</i>, <i>CsTRXh1</i>, <i>CsTRXm1</i>, <i>CsTRXo3</i>, <i>CsTRXx2</i> and <i>CsTRXy1</i> were observed to be reduced upon pathogen infection. Subcellular localization analysis found that CsTRXf1, CsTRXm1, CsTRXo3, CsTRXx2 and CsTRXy1 were predominantly localized in chloroplasts, whereas CsTRXh1 was distributed indiscriminately. This research yields integral data on <i>CsTRXs</i>, facilitating future efforts to decipher the gene functions of <i>CsTRXs</i>.
DOI: 10.6084/m9.figshare.24886565.v1
title: Systematic analysis of the thioredoxin gene family in <i> Citrus sinensis</i>: identification, phylogenetic analysis, and gene expression patterns

description: Thioredoxin (TRX) proteins play essential roles in reactive oxygen species scavenging in plants. We executed an exhaustive analysis of the TRX gene family in <i>Citrus sinensis</i> (<i>CsTRXs</i>), encompassing identification, phylogenetic analysis, detection of conserved motifs and domains, gene structure, cis-acting elements, gene expression trends, and subcellular localization analysis. Our findings established that a total of 22 <i>CsTRXs</i> with thioredoxin domains were identified in the genome of <i>C. sinensis</i>. Phylogenetic analysis indicated that CsTRXs were divided into six subclusters. Conserved motifs analysis of CsTRXs indicated a wide range of conserved motifs. A significant number of cis-acting elements associated with both abiotic and biotic stress responses, inclusive of numerous phytohormone-related elements, were detected in the promoter regions of <i>CsTRXs</i>. The expression levels of <i>CsTRXs</i> including <i>CsTRXf1</i>, <i>CsTRXh1</i>, <i>CsTRXm1</i>, <i>CsTRXo3</i>, <i>CsTRXx2</i> and <i>CsTRXy1</i> were observed to be reduced upon pathogen infection. Subcellular localization analysis found that CsTRXf1, CsTRXm1, CsTRXo3, CsTRXx2 and CsTRXy1 were predominantly localized in chloroplasts, whereas CsTRXh1 was distributed indiscriminately. This research yields integral data on <i>CsTRXs</i>, facilitating future efforts to decipher the gene functions of <i>CsTRXs</i>.
DOI: 10.6084/m9.figshare.14060858
title: PCID2, a subunit of the <i>Drosophila</i> TREX-2 nuclear export complex, is essential for both mRNA nuclear export and its subsequent cytoplasmic trafficking

description: The TREX-2 complex is essential for the general nuclear mRNA export in eukaryotes. TREX-2 interacts with the nuclear pore and transcriptional apparatus and links transcription to the mRNA export. However, it remains poorly understood how the TREX-2-dependent nuclear export is connected to the subsequent stages of mRNA trafficking. Here, we show that the PCID2 subunit of <i>Drosophila</i> TREX-2 is present in the cytoplasm of the cell. The cytoplasmic PCID2 directly interacts with the NudC protein and this interaction maintains its stability in the cytoplasm. Moreover, PCID2 is associated with the cytoplasmic mRNA and microtubules. The PCID2 knockdown blocks nuclear export of mRNA and also affects the general mRNA transport into the cytoplasm. These data suggest that PCID2 could be the link between the nuclear TREX-2-dependent export and the subsequent cytoplasmic trafficking of mRNA.
DOI: 10.6084/m9.figshare.13625240
title: Hypoxia activated long non-coding RNA HABON regulates the growth and proliferation of hepatocarcinoma cells by binding to and antagonizing HIF-1 alpha

description: The adaptation of tumour cells to hypoxic microenvironment is one of the most significant characteristics of many malignant tumour diseases including hepatocarcinoma. Recently, long non-coding RNAs (lncRNAs) have been reported to play important roles in the various levels of gene regulation thus functioning in growth and survival of tumour cells. Here, new hypoxia-related lncRNAs in hepatocarcinoma cells were screened and validated by lncRNA chip-array as well as real-time RT-PCR. Among them, a hypoxia-activated lncRNA that we identified and termed Hypoxia-Activated BNIP3 Overlapping Non-coding RNA (HABON), was not only regulated by hypoxic-induced factor-1α (HIF-1α) but its expression increased significantly under hypoxia in tumour cells. We deciphered the biological characteristics of HABON including its cell localization, genomic location, as well as its full-length sequence, and proved HABON could promote growth, proliferation and clone-formation of hepatocarcinoma cells under hypoxia. Then, we revealed that HABON was transcriptionally activated by HIF-1α in hypoxic cells, furthermore, it could interact with HIF-1α and promote its protein degradation, thus affecting transcription of HIF-1α’s target genes to exert its effects on cells. Besides, the elevated expression of HABON under hypoxia could promote the transcriptional activation of BNIP3 through HIF-1α, and increasing the expression level of BNIP3. This research provides a novel clue for the adaptive survival and growth mechanism of tumour under hypoxia, and gives a way to reveal the nature of tumour cells’ resistance characteristics to harsh microenvironment.
DOI: 10.6084/m9.figshare.13625240.v1
title: Hypoxia activated long non-coding RNA HABON regulates the growth and proliferation of hepatocarcinoma cells by binding to and antagonizing HIF-1 alpha

description: The adaptation of tumour cells to hypoxic microenvironment is one of the most significant characteristics of many malignant tumour diseases including hepatocarcinoma. Recently, long non-coding RNAs (lncRNAs) have been reported to play important roles in the various levels of gene regulation thus functioning in growth and survival of tumour cells. Here, new hypoxia-related lncRNAs in hepatocarcinoma cells were screened and validated by lncRNA chip-array as well as real-time RT-PCR. Among them, a hypoxia-activated lncRNA that we identified and termed Hypoxia-Activated BNIP3 Overlapping Non-coding RNA (HABON), was not only regulated by hypoxic-induced factor-1α (HIF-1α) but its expression increased significantly under hypoxia in tumour cells. We deciphered the biological characteristics of HABON including its cell localization, genomic location, as well as its full-length sequence, and proved HABON could promote growth, proliferation and clone-formation of hepatocarcinoma cells under hypoxia. Then, we revealed that HABON was transcriptionally activated by HIF-1α in hypoxic cells, furthermore, it could interact with HIF-1α and promote its protein degradation, thus affecting transcription of HIF-1α’s target genes to exert its effects on cells. Besides, the elevated expression of HABON under hypoxia could promote the transcriptional activation of BNIP3 through HIF-1α, and increasing the expression level of BNIP3. This research provides a novel clue for the adaptive survival and growth mechanism of tumour under hypoxia, and gives a way to reveal the nature of tumour cells’ resistance characteristics to harsh microenvironment.
DOI: 10.6084/m9.figshare.13526195
title: A chromatin-associated splicing isoform of <i>OIP5-AS1</i> acts in <i>cis</i> to regulate the <i>OIP5</i> oncogene

description: A large portion of the human genome is transcribed into long noncoding RNAs that can range from 200 nucleotides to several kilobases in length. The number of identified lncRNAs is still growing, but only a handful of them have been functionally characterized. However, it is known that the functions of lncRNAs are closely related to their subcellular localization. Cytoplasmic lncRNAs can regulate mRNA stability, affect translation and act as miRNA sponges, while nuclear-retained long noncoding RNAs have been reported to be involved in transcriptional control, chromosome scaffolding, modulation of alternative splicing and chromatin remodelling. Through these processes, lncRNAs have diverse regulatory roles in cell biology and diseases. <i>OIP5-AS1</i> (also known as <i>Cyrano</i>), a poorly characterized lncRNA expressed antisense to the <i>OIP5</i> oncogene, is deregulated in multiple cancers. We showed that one of the <i>OIP5-AS1</i> splicing forms (ENST00000501665.2) is retained in the cell nucleus where it associates with chromatin, thus narrowing down the spectrum of its possible mechanisms of action. Its knockdown with antisense LNA gapmeRs led to inhibited expression of a sense partner, <i>OIP5</i>, strongly suggesting a functional coupling between <i>OIP5</i> and ENST00000501665.2. A subsequent bioinformatics analysis followed by RAP-MS and RNA Immunoprecipitation experiments suggested its possible mode of action; in particular, we found that ENST00000501665.2 directly binds to a number of nuclear proteins, including SMARCA4, a component of the SWI/SNF chromatin remodelling complex, whose binding motif is located in the promoter of the <i>OIP5</i> oncogene.
DOI: 10.6084/m9.figshare.14060858.v1
title: PCID2, a subunit of the <i>Drosophila</i> TREX-2 nuclear export complex, is essential for both mRNA nuclear export and its subsequent cytoplasmic trafficking

description: The TREX-2 complex is essential for the general nuclear mRNA export in eukaryotes. TREX-2 interacts with the nuclear pore and transcriptional apparatus and links transcription to the mRNA export. However, it remains poorly understood how the TREX-2-dependent nuclear export is connected to the subsequent stages of mRNA trafficking. Here, we show that the PCID2 subunit of <i>Drosophila</i> TREX-2 is present in the cytoplasm of the cell. The cytoplasmic PCID2 directly interacts with the NudC protein and this interaction maintains its stability in the cytoplasm. Moreover, PCID2 is associated with the cytoplasmic mRNA and microtubules. The PCID2 knockdown blocks nuclear export of mRNA and also affects the general mRNA transport into the cytoplasm. These data suggest that PCID2 could be the link between the nuclear TREX-2-dependent export and the subsequent cytoplasmic trafficking of mRNA.
DOI: 10.6084/m9.figshare.13378777
title: Hormonal regulation of microRNA expression dynamics in the gut of the yellow fever mosquito <i>Aedes aegypti</i>

description: The yellow fever mosquito <i>Aedes aegypti</i> is an obligatory blood feeder and a major arboviral disease vector, evoking severe public health concerns worldwide. In adult female mosquitoes, the gut is critical for blood digestion and pathogen entry. We aimed for a systematic exploration of microRNA expression dynamics in the gut during the gonadotrophic cycle. Small RNA libraries were constructed from female mosquito gut tissues at five time points. Unsupervised hierarchical clustering revealed three expression clusters (early, mid and late) peaking at sequential time points – 24, 48 and 72 h posteclosion. Differentially expressed miRNAs were identified at 24 h post-blood meal (PBM). Depletions of Methoprene-tolerant [Met; the juvenile hormone (JH) receptor] and Ecdysone receptor [EcR; the receptor to 20-hydroxyecdysone (20E)] were performed using dsRNA to these genes to investigate impacts on microRNA expressions. Our results suggest that Met-mediated signalling downregulates miRNA expression from the early cluster and upregulates that from the late cluster. EcR signalling either up- or downregulated miRNA levels at 24 h PBM, indicating a differential effect of this receptor in miRNA gene expression. Furthermore, miR-281, which is the most abundant miRNA in the gut tissue, is induced and repressed by Met- and EcR-mediated signalling, respectively. Systematic depletion using synthetic antagomir and phenotype examinations indicate that miR-281 is obligatory for the normal progression of blood digestion, ovarian development and reproduction. Collectively, this study unveils expression dynamics of microRNAs in the female gut tissue during the gonadotrophic cycle and demonstrates that they are affected by JH and 20E signalling.