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Starch degradation is a necessary process determining banana fruit quality during ripening. Many starch degradation-related genes are well studied. However, the transcriptional regulation of starch degradation during banana fruit ripening remains poorly understood. In this study, we identified a MYB transcription factor (TF) termed MaMYB3, as a putative protein binding the promoter of MaGWD1, a member of glucan water dikinase (GWD) family which has been demonstrated as an important enzyme of starch degradation. MaMYB3 was ripening- and ethylene-repressible, and its expression was negatively correlated with starch degradation. Acting as a nucleus-localized transcriptional repressor, MaMYB3 repressed the transcription of 10 starch degradation-related genes, including MaGWD1, MaSEX4, MaBAM7-MaBAM8, MaAMY2B, MaAMY3, MaAMY3A, MaAMY3C, MaMEX1, and MapGlcT2-1, by directly binding to their promoters. Interestingly, a previously identified activator of starch degradation-related genes, MabHLH6, was also suppressed by MaMYB3. The ectopic overexpression of MaMYB3 in tomato down-regulated the expression of starch degradation-related genes, inhibited starch degradation and delayed fruit ripening. Based on these findings, we conclude that MaMYB3 negatively impacts starch degradation by directly repressing starch degradation-related genes and MabHLH6, and thereby delays banana fruit ripening. Collectively, our study expands our understanding of the complex transcriptional regulatory hierarchy modulating starch degradation during fruit ripening.

Both NAC transcription factors (TFs) and reactive oxygen species (ROS) are known to be involved in leaf senescence. However, how NAC TFs modulate ROS metabolism associated with leaf senescence remains largely uncharacterized, especially during leaf senescence of postharvest economically leafy vegetables such as Chinese flowering cabbage. Here, we found that expression levels of two genes BrRbohB and BrRbohC-like encoding ROS-producing enzymes respiratory burst oxidase homologues (RBOHs) were increased consistently with the progression of postharvest leaf senescence, exhibiting a good correlation with ROS accumulation and chlorophyll degradation, as well as expressions of two chlorophyll catabolic genes ( CCGs), BrNYC1 and BrNYE1. Significantly, a novel, nuclear-localized transcriptional activator BrNAC055 was identified, and observed to show a similar expression pattern with BrRbohB, BrRbohC-like, BrNYC1 and BrNYE1. Further gel mobility shift and dual luciferase reporter assays confirmed that BrNAC055 bound directly to the NAC binding sequence (NACBS) in BrRbohB, BrRbohC-like, BrNYC1, and BrNYE1 promoters, and activated their activities. Moreover, transient overexpression of BrNAC055 in tobacco leaves made an increased ROS level and accelerated chlorophyll degradation via the up-regulation of NbRbohA and NbSGR1, resulting in the promoted leaf senescence. On the basis of these findings, we conclude that BrNAC055 acts as a transcriptional activator of ROS production and chlorophyll degradation by activating the transcriptions of RBOHs and CCGs and thereby accelerates leaf senescence in Chinese flowering cabbage.

Chloroplast development and chlorophyll(Chl)metabolism in unripe tomato contribute to the growth and quality of the fruit, however these mechanisms are poorly understood. In this study, we initially investigated seven homeobox-containing transcription factors (TFs) with specific ripening-associated expression patterns using virus-induced gene silencing (VIGS) technology and found that inhibiting the expression of one of these TFs, BEL1-LIKE HOMEODOMAIN11 (SlBEL11), significantly increased Chl levels in unripe tomato fruit. This enhanced Chl accumulation was further validated by generating stable RNA interference (RNAi) transgenic lines. RNA sequencing (RNA-seq) of RNAi-SlBEL11 fruit at the mature green (MG) stage showed that 48 genes involved in Chl biosynthesis, photosynthesis and chloroplast development were significantly upregulated compared with the wild type (WT) fruit. Genomic global scanning for Homeobox TF binding sites combined with RNA-seq differential gene expression analysis showed that 22 of these 48 genes were potential target genes of SlBEL11 protein. These genes included Chl biosynthesis-related genes encoding for protochlorophyllide reductase (POR), magnesium chelatase H subunit (CHLH) and chlorophyllide a oxygenase (CAO), and chloroplast development-related genes encoding for chlorophyll a/b binding protein (CAB), homeobox protein knotted 2 (TKN2) and ARABIDOPSIS PSEUDO RESPONSE REGULATOR 2-LIKE (APRR2-like). Electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation quantitative polymerase chain reaction (PCR) (ChIP-qPCR) assays were employed to verify that SlBEL11 protein could bind to the promoters for TKN2, CAB and POR. Taken together, our findings demonstrated that SlBEL11 plays an important role in chloroplast development and Chl synthesis in tomato fruit.

The 186 aa truncated protein produced by the tomato spontaneous non-ripening (nor) mutant enters the nucleus and combines with the promoters of its target genes, resulting in a gain of function., The tomato non-ripening (nor) mutant generates a truncated 186-amino-acid protein (NOR186) and has been demonstrated previously to be a gain-of-function mutant. Here, we provide more evidence to support this view and answer the open question of whether the NAC-NOR gene is important in fruit ripening. Overexpression of NAC-NOR in the nor mutant did not restore the full ripening phenotype. Further analysis showed that the truncated NOR186 protein is located in the nucleus and binds to but does not activate the promoters of 1-aminocyclopropane-1-carboxylic acid synthase2 (SlACS2), geranylgeranyl diphosphate synthase2 (SlGgpps2), and pectate lyase (SlPL), which are involved in ethylene biosynthesis, carotenoid accumulation, and fruit softening, respectively. The activation of the promoters by the wild-type NOR protein can be inhibited by the mutant NOR186 protein. On the other hand, ethylene synthesis, carotenoid accumulation, and fruit softening were significantly inhibited in CR-NOR (CRISPR/Cas9-edited NAC-NOR) fruit compared with the wild-type, but much less severely affected than in the nor mutant, while they were accelerated in OE-NOR (overexpressed NAC-NOR) fruit. These data further indicated that nor is a gain-of-function mutation and NAC-NOR plays a significant role in ripening of wild-type fruit.

Background Congenital cataract is the most common cause of blindness among children worldwide. The aim of this study was to identify causative mutations in a Chinese family with isolated autosomal dominant posterior subcapsular cataract. Methods The proband and her parents underwent full ophthalmological examinations. DNA was extracted from the participants’ peripheral venous blood. The mutation was identified via panel-based next-generation sequencing (NGS) and was validated via Sanger sequencing. Results Posterior subcapsular lenticular opacity was observed in both of the proband’s eyes. The novel deletion mutation c.797_814del, p.Ser266_Ala271del in the PITX3 gene was identified in the proband and her father. This mutation is located within the otp/aristaless/rax (OAR) domain at the COOH-terminus of the protein, which functions in DNA binding and transactivation. This mutation would result in a deletion of 6 amino acid residues at the C terminal of the protein. Conclusions The mutation c.797_814del, p.Ser266_Ala271del is a novel mutation in the conserved DNA-binding OAR domain of PITX3 that causes congenital cataract. Electronic supplementary material The online version of this article (10.1186/s12881-019-0782-2) contains supplementary material, which is available to authorized users.

Melatonin and abscisic acid (ABA) play contrasting roles in regulating leaf senescence in plants. The molecular mechanism underlying the interaction between melatonin and ABA involved in leaf senescence, however, remains poorly defined. Herein, we found that exogenous application of melatonin delayed the senescence of Chinese flowering cabbage, accompanied by reduced expression of chlorophyll catabolic and ABA biosynthetic genes, and a lower endogenous ABA level. Significantly, three nucleus-localized transcriptional activators BrABF1, BrABF4, and BrABI5 were identified, and their expressions were repressed by melatonin. In vitro and in vivo binding experiments revealed that BrABF1, BrABF4, and BrABI5 activated the transcription of a series of ABA biosynthetic and chlorophyll catabolic genes by physically binding to their promoters. Moreover, transient over-expression of BrABF1, BrABF4, and BrABI5 in tobacco leaves induced ABA accumulation and promoted chlorophyll degradation by upregulating tobacco ABA biosynthetic and chlorophyll catabolic genes, resulting in the accelerated leaf senescence. These effects were significantly attenuated by melatonin treatment. Our findings suggest that melatonin-mediated inhibition of leaf senescence involves suppression of ABFs-mediated ABA biosynthesis and chlorophyll degradation. Unraveling of the molecular regulatory mechanism of leaf senescence controlled by ABA and melatonin expands our understanding of the regulation of this phenomenon and offers potentially more effective molecular breeding strategies for extending the shelf-life of Chinese flowering cabbage.

Papaya fruits accumulate carotenoids during fruit ripening. Although many papaya carotenoid biosynthesis pathway genes have been identified, the transcriptional regulators of these genes have not been characterized. In this study, a NAC transcription factor, designated as CpNAC1, was characterized from papaya fruit. CpNAC1 was localized exclusively in nucleus and possessed transcriptional activation activity. Expression of carotenoid biosynthesis genes phytoene desaturases (CpPDSs) and CpNAC1 was increased during fruit ripening and by propylene treatment, which correlates well with the elevated carotenoid content in papaya. The gel mobility shift assays and transient expression analyses demonstrated that CpNAC1 directly binds to the NAC binding site (NACBS) motifs in CpPDS2/4 promoters and activates them. Collectively, these data suggest that CpNAC1 may act as a positive regulator of carotenoid biosynthesis during papaya fruit ripening possibly via transcriptional activation of CpPDSs such as CpPDS2/4.

Phytohormone gibberellin (GA) and plant-specific WRKY transcription factors (TFs) are reported to play important roles in leaf senescence. The association of WRKY TFs with GA-mediated leaf senescence of economically important leafy vegetables like Chinese flowering cabbage, however, remains largely unknown. In this study, we showed that exogenous application of GA3 suppressed Chinese flowering cabbage leaf senescence, with GA3-treated cabbages maintaining a higher level of maximum quantum yield (Fv/Fm) and total chlorophyll content. GA3 treatment also led to lower electrolyte leakage and expression level of a series of senescence-associated genes (SAGs) including BrSAG12 and BrSAG19, and chlorophyll catabolic genes (CCGs) BrPPH1, BrNYC1, and BrSGRs. In addition, higher transcription levels of GA biosynthetic genes BrKAO2 and BrGA20ox2 were found after GA3 treatment. More importantly, a GA-repressible, nuclear-localized WRKY TF, BrWRKY6, a homologue of the Arabidopsis AtWRKY6, was identified and characterized. BrWRKY6 was GA-repressible and localized in the nucleus. Further experiments revealed that BrWRKY6 repressed the expression of BrKAO2 and BrGA20ox2, while it activated BrSAG12, BrNYC1, and BrSGR1, through binding to their promoters via the W-box cis-element. Together, the novel GA-WRKY link reported in our study provides new insight into the transcriptional regulation of GA-suppressed leaf senescence in Chinese flowering cabbage.

Microarray expression analysis was used to forecast the roles of differentially co-expressed genes (DCG) and DCG and links in the pathogenesis of prostate cancer. In addition, we demonstrate that the relationship between transcriptional factors (TFs) and their targets can be considered a key factor in determining the difference between primary and metastatic prostate cancer. Regulatory impact factors were adopted to calculate the impact of TF. We identified 5 TFs and 29 target genes important in the transition between normal prostate and primary prostate cancer and 2 TFs and 7 target genes important in the transition between primary and metastatic prostate cancer. These results suggest that it may be possible to predict the clinical behavior of prostate cancer based on gene expression analysis.

Subset heterogeneity of the mononuclear phagocyte system (MPS) is controlled by defined transcriptional networks and programs; however, the dynamic establishment of programs that control broad, orchestrated expression of transcription factors (TFs) during the progression of monocyte-into-phagocyte (MP) differentiation remains largely unexplored. By using chromatin immunoprecipitation assays, we show the extensive trimethylation of histone H3 lysine 4 (H3K4me3) as well as histone H3 lysine 27 (H3K27me3) occupancy with broad footprints at the promoters of MP differentiation-related TFs, such as HOXA and FOXO genes, KLF4, IRF8 and others. The rapid repression of HOXA genes was closely associated with the MP differentiation program. H3K4me3 participates in regulating HOXA genes at mild and terminal differentiation periods, while H3K27me3 maintains low-level expression of HOXA genes at phagocytic maintenance periods. Furthermore, the reprogramming of H3K27me3 plays a major role in the up-regulation of KLF4 and FOXO genes during MP differentiation. Importantly, the pharmacological inhibition of H3K4me3 and/or H3K27me3 strikingly promotes the differentiation programs of THP-1 and K562 cells. Together, these findings elucidate mechanisms crucial to the dynamic establishment of epigenetic memory, which is central to the maintenance of the MP differentiation blockade.

Plant-specific WRKY transcription factors (TFs) have been implicated to function as regulators of leaf senescence, but their association with postharvest leaf senescence of economically important leafy vegetables, is poorly understood. In this work, the characterization of a Group IIe WRKY TF, BrWRKY65, from Chinese flowering cabbage (Brassica rapa var. parachinensis) is reported. The expression of BrWRKY65 was up-regulated following leaf chlorophyll degradation and yellowing during postharvest senescence. Subcellular localization and transcriptional activation assays showed that BrWRKY65 was localized in the nucleus and exhibited trans-activation ability. Further electrophoretic mobility shift assay (EMSA) and transient expression analysis clearly revealed that BrWRKY65 directly bound to the W-box motifs in the promoters of three senescence-associated genes (SAGs) such as BrNYC1 and BrSGR1 associated with chlorophyll degradation, and BrDIN1, and subsequently activated their expressions. These findings demonstrate that BrWRKY65 may be positively associated with postharvest leaf senescence, at least partially, by the direct activation of SAGs. Taken together, these findings provide new insights into the transcriptional regulatory mechanism of postharvest leaf senescence in Chinese flowering cabbage.

The yeast transcriptional coactivator GCN5 (yGCN5), a histone acetyltransferase (HAT), is part of large multimeric complexes that are required for chromatin remodeling and transcriptional activation. Like other eukaryotes, the malaria parasite DNA is organized into nucleosomes and the genome encodes components of chromatin-remodeling complexes. Here we show that GCN5 is conserved in Plasmodium species and that the most homologous regions are within the HAT domain and the bromodomain. The Plasmodium falciparum GCN5 homologue ( PfGCN5 ) is spliced with three introns, encoding a protein of 1,464 residues. Mapping of the ends of the PfGCN5 transcript suggests that the mRNA is 5.2 to 5.4 kb, consistent with the result from Northern analysis. Using free core histones, we determined that recombinant PfGCN5 proteins have conserved HAT activity with a substrate preference for histone H3. Using substrate-specific antibodies, we determined that both Lys-8 and -14 of H3 were acetylated by the recombinant PfGCN5. In eukaryotes, GCN5 homologues interact with yeast ADA2 homologues and form large multiprotein HAT complexes. We have identified an ADA2 homologue in P. falciparum , PfADA2. Yeast two-hybrid and in vitro binding assays verified the interactions between PfGCN5 and PfADA2, suggesting that they may be associated with each other in vivo. The conserved function of the HAT domain in PfGCN5 was further illustrated with yeast complementation experiments, which showed that the PfGCN5 region corresponding to the full-length yGCN5 could partially complement the yGCN5 deletion mutation. Furthermore, a chimera comprising the PfGCN5 HAT domain fused to the remainder of yeast GCN5 (yGCN5) fully rescued the yGCN5 deletion mutant. These data demonstrate that PfGCN5 is an authentic GCN5 family member and may exist in chromatin-remodeling complexes to regulate gene expression in P. falciparum .

The transcriptional coactivator ADA2 is an evolutionarily conserved component of histone acetyltransferase (HAT) complexes involved in chromatin remodeling and transcriptional regulation in eukaryotes. The Plasmodium falciparum homologue, PfADA2, has a 7737 bp open reading frame, encoding a protein of 2578 amino acids with an ADA2-like domain located near the C-terminus. The annotated PfADA2 in the parasite genome is Pf10_143, located on chromosome 10. Sequence analysis demonstrated the presence of an ADA2 homologue in each Plasmodium species selected for genome sequencing. Mapping of the 5' transcriptional initiation sites suggested that PfADA2 transcription was initiated from multiple sites. Northern analysis detected a major transcript of approximately 8.5 kb in erythrocytic stage parasites. An antiserum raised against the internal ADA2-like domain detected multiple proteins from mixed blood stages, suggesting that PfADA2 may be proteolytically processed. In comparison, affinity-purified anti-GCN5 antibodies reacted with a major protein of approximately 200 kDa and immunoprecipitated proteins from the parasite lysate with HAT activity similar to that of the recombinant GCN5. Moreover, this GCN5-like HAT activity could also be precipitated with anti-PfADA2 antibodies, indicating that PfADA2 is associated with PfGCN5 in vivo. To illustrate whether PfADA2 could functionally replace the yADA2, complementation experiments were performed. However, the ADA2-like domain of PfADA2 failed to rescue the yeast ada2(-) mutant, probably due to significant divergence between the two genes. Taken together, these results indicate the presence of PfADA2-PfGCN5 complex(es) in the malaria parasite, which may have conserved functions in chromatin remodeling and gene regulation.