Regulatory Peptide Encoded by the Primary Transcript of miR396a Influences Gene Expression and Root Development in Solanum lycopersicum.

MicroRNAs (miRNAs) are the processing products of primary miRNAs (pri-miRNAs) that regulate the expression of target genes. Recent studies have demonstrated that some pri-miRNAs can encode small peptides (miPEPs) that perform significant biological functions. The function of miPEPs in tomatoes, an important model horticultural crop, remains to be investigated. Here, we characterized the primary sequence of tomato miR396a using 5' RACE and confirmed the presence of miPEP396a in tomato by verifying the translational activity of the start codon. It primarily resides in the nucleus to exert its function and additionally regulates the expression of pri-miR396a, miR396a, and its target genes. Transcriptomic and metabolomic analyses showed that in vitro synthesis of miPEP396a significantly increased the expression of genes related to phenylpropanoid biosynthesis and hormones in tomato. Meanwhile, our in vitro application of miPEP396a in tomato significantly inhibited the elongation of tomato primary roots. In conclusion, our results indicate that miPEP396a regulates root growth in tomato by specifically promoting miR396a expression, provide insight into the function of miPEPs in tomato and potential applications.

A sensitive coumarin fluorescence sensor designed for isoprene detection and imaging research in plants.

The release of isoprene by plants is considered to be an adaptation to the environment. Herein, a highly selective coumarin fluorescent probe (DMIC) was designed for detecting isoprene. When isoprene came into contact with the maleimide of DMIC, an electrophilic addition process took place. The powerful push-pull effect of DMIC was disrupted. Simultaneously, intramolecular charge transfer was initiated. This enabled DMIC to achieve rapid detection of isoprene within 5 min. Furthermore, excellent linearity was observed in the concentration range of 1-560 ppm (R2 = 0.996). A limit of detection is 1.6 ppm. DMIC was applied to in vitro studies of plant release of liberated isoprene. By monitoring the release of isoprene from different tree species throughout the day, the dynamics of isoprene release from plants throughout the day have been successfully revealed. In addition, the release of isoprene varied considerably among different tree species. In particular, the biocompatibility of DMIC allowed for the in vivo detection of isoprene using fluorescence imaging. The results successfully revealed the dynamics of isoprene release in plants under stress. The amount of isoprene that a plant produced increased with the severity of the stress it experienced. This suggested that the level of isoprene content in plants could be used as a preliminary indicator of the physiological health status of plants. This research demonstrates great potential for clarifying signal transduction in biological systems. It provided ideas for further understanding the biology of isoprene.

Dual-functionalization of fluorescent carbon dots via cyclodextrin and aminosilane for visual detection of ß-glucuronidase and bioimaging.

A sensitive method for the detection of ß-glucuronidase was established using functionalized carbon dots (ß-CD-SiCDs) as fluorescent probes. The ß-CD-SiCDs were found to be obtained through in situ autopolymerization by mixing the solutions of methyldopa, mono-6-ethylenediamine-ß-cyclodextrin and N-(ß-aminoethyl)-γ-aminopropyltrimethoxysilane at room temperature. The method has the characteristics of low energy consumption, simple and rapid. ß-CD-SiCDs exhibited green fluorescence at 515 nm emission with a quantum yield of 7.9 %. 4-nitrophenyl-ß-D-glucuronide was introduced as a substrate for ß-glucuronidase to generate p-nitrophenol. Subsequently, p-nitrophenol self-assembled with ß-CD-SiCDs through host-guest recognition to form a stable inclusion complex, resulting in the fluorescence quenching of ß-CD-SiCDs. The linear range of ß-CD-SiCDs for detecting ß-glucuronidase activity was 0.5-60 U L-1 with a detection limit of 0.14 U L-1. For on-site detection, gel reagents were prepared by a simple method and the images were visualized and quantified by taking advantage of smartphones, avoiding the use of large instrumentation. The constructed fluorescence sensing platform has the benefits of easy operation and time saving, and has been successfully used for the detection of ß-glucuronidase activity in serum and cell imaging.

The effectors of Phytophthora infestans impact host immunity upon regulation of antagonistic hormonal activities.

MAIN CONCLUSION: Phytophthora infestans effectors manipulate the antagonism of host hormones to interfere with the immune response of plants at different infection stages. Phytophthora infestans (P. infestans) poses a serious threat to global crop production, and its effectors play an indispensable role in its pathogenicity. However, the function of these effectors during the switch from biotrophy to necrotrophy of P. infestans remains unclear. Further research on the effectors that manipulate the antagonistic response of host hormones is also lacking. In this study, a coexpression analysis and infection assays were performed to identify distinct gene expression changes in both P. infestans and tomato. During the switch from biotrophy to necrotrophy, P. infestans secretes three types of effectors to interfere with host salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA) levels. The three aforementioned effectors also regulate the host gene expression including NPR1, TGA2.1, PDF1.2, NDR1, ERF3, NCED6, GAI4, which are involved in hormone crosstalk. The changes in plant hormones are mediated by the three types of effectors, which may accelerate infection and drive completion of the P. infestans lifecycle. Our findings provide new insight into plant‒pathogen interactions that may contribute to the prevention growth of hemibiotrophic pathogens.

Sl-lncRNA47980, a positive regulator affects tomato resistance to Phytophthora infestans.

Emerging evidence suggests that long non-coding RNAs (lncRNAs) involve in defense respond against pathogen attack and show great potentials to improve plant resistance. Tomato late blight, a destructive plant disease, is caused by the oomycete pathogen Phytophthora infestans, which seriously affects the yield and quality of tomato. Our previous research has shown that Sl-lncRNA47980 is involved in response to P. infestans infection, but its molecular mechanism is unknown. Gain- and loss-of-function experiments revealed that Sl-lncRNA47980 as a positive regulator, played a crucial role in enhancing tomato resistance to P. infestans. The Sl-lncRNA47980-overexpressing transgenic plants exhibited an improved ability to scavenge reactive oxygen species (ROS), decreased contents of endogenous gibberellin (GA) and salicylic acid (SA), and increased contents of jasmonic acid (JA), while silencing of Sl-lncRNA47980 showed an opposite trend in the levels of these hormones. Furthermore, it was found that Sl-lncRNA47980 could upregulate the expression of SlGA2ox4 gene through activation of the promoter of SlGA2ox4 to affect GA content. The increased expression of the tomato GA signaling repressor SlDELLA could activate JA-related genes and inhibit SA-related genes to varying degrees respectively. In addition, exogenous application of GA3 and GA synthesis inhibitor uniconazole could increase disease susceptibility of Sl-lncRNA47980-overexpressing plants and the resistance of Sl-lncRNA47980-silenced plants, respectively, to P. infestans. From thus, it was speculated that Sl-lncRNA47980 conferred tomato resistance to P. infestans, which was related to the decrease in endogenous GA content. Our study provided information to link Sl-lncRNA47980 with changes in ROS accumulation and phytohormone levels in plant immunity, thus providing a new candidate gene for tomato breeding.

H2O2/O2 self-supply and Ca2+ overloading MOF-based nanoplatform for cascade-amplified chemodynamic and photodynamic therapy.

Introduction: Reactive oxygen species (ROS)-mediated therapies have typically been considered as noninvasive tumor treatments owing to their high selectivity and efficiency. However, the harsh tumor microenvironment severely impairs their efficiency. Methods: Herein, the biodegradable Cu-doped zeolitic imidazolate framework-8 (ZIF-8) was synthesized for loading photosensitizer Chlorin e6 (Ce6) and CaO2 nanoparticles, followed by surface decoration by hyaluronic acid (HA), obtaining HA/CaO2-Ce6@Cu-ZIF nano platform. Results and Discussion: Once HA/CaO2-Ce6@Cu-ZIF targets tumor sites, the degradation of Ce6 and CaO2 release from the HA/CaO2-Ce6@Cu-ZIF in response to the acid environment, while the Cu2+ active sites on Cu-ZIF are exposed. The released CaO2 decompose to generate hydrogen peroxide (H2O2) and oxygen (O2), which alleviate the insufficiency of intracellular H2O2 and hypoxia in tumor microenvironment (TME), effectively enhancing the production of hydroxyl radical (•OH) and singlet oxygen (1O2) in Cu2+-mediated chemodynamic therapy (CDT) and Ce6-induced photodynamic therapy (PDT), respectively. Importantly, Ca2+ originating from CaO2 could further enhance oxidative stress and result in mitochondrial dysfunction induced by Ca2+ overloading. Conclusion: Thus, the H2O2/O2 self-supplying and Ca2+ overloading ZIF-based nanoplatform for cascade-amplified CDT/PDT synergistic strategy is promising for highly efficient anticancer therapy.

Unveiling the secrets of non-coding RNA-encoded peptides in plants: A comprehensive review of mining methods and research progress.

Non-coding RNAs (ncRNAs) are not conventionally involved in protein encoding. However, recent findings indicate that ncRNAs possess the capacity to code for proteins or peptides. These ncRNA-encoded peptides (ncPEPs) are vital for diverse plant life processes and exhibit significant potential value. Despite their importance, research on plant ncPEPs is limited, with only a few studies conducted and less information on the underlying mechanisms, and the field remains in its nascent stage. This manuscript provides a comprehensive overview of ncPEPs mining methods in plants, focusing on prediction, identification, and functional analysis. We discuss the strengths and weaknesses of various techniques, identify future research directions in the ncPEPs domain, and elucidate the biological functions and agricultural application prospects of plant ncPEPs. By highlighting the immense potential and research value of ncPEPs, we aim to lay a solid foundation for more in-depth studies in plant science.

Genome-wide identification and characterization of the tomato F-box associated (FBA) protein family and expression analysis of their responsiveness to Phytophthora infestans.

Late blight caused by Phytophthora infestans brings huge economic losses to the production of tomato (Solanum lycopersicum) every year. F-box proteins participate in plants response to phytohormones and biotic stress, whereas as the largest subfamily of F-box superfamily, the detailed information about F-box associated (SlFBA) family in tomato has been rarely reported. In this study, a total of 46 tomato FBA genes were identified based on the latest genome annotation. Phylogenetic analysis revealed that the FBA proteins from tomato and 6 different plant species were clustered into 7 distinct clades. The SlFBA genes were unevenly distributed on 11 chromosomes of tomato, mainly concentrated in the regions with high gene density. Tandem duplications and purification selection contribute to the expansion and evolution of the SlFBA gene family. Transcriptome analysis revealed that the SlFBA genes were differentially expressed in different tissues with obvious tissue-specific expression patterns. There were 18 SlFBA genes differentially expressed in P. infestans-resistant and -susceptible tomato, among which, 3 SlFBA genes might play positive roles in tomato resistance to P. infestans. Taken together, this study systematically analyzed the SlFBA genes family for the first time and identified the candidate SlFBA genes that affect tomato resistance to P. infestans, which provided important genetic and breeding resources for improving tomato resistance to pathogens.

Mining plant endogenous target mimics from miRNA-lncRNA interactions based on dual-path parallel ensemble pruning method.

The interactions between microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) play important roles in biological activities. Specially, lncRNAs as endogenous target mimics (eTMs) can bind miRNAs to regulate the expressions of target messenger RNAs (mRNAs). A growing number of studies focus on animals, but the studies on plants are scarce and many functions of plant eTMs are unknown. This study proposes a novel ensemble pruning protocol for predicting plant miRNA-lncRNA interactions at first. It adaptively prunes the base models based on dual-path parallel ensemble method to meet the challenge of cross-species prediction. Then potential eTMs are mined from predicted results. The expression levels of RNAs are identified through biological experiment to construct the lncRNA-miRNA-mRNA regulatory network, and the functions of potential eTMs are inferred through enrichment analysis. Experiment results show that the proposed protocol outperforms existing methods and state-of-the-art predictors on various plant species. A total of 17 potential eTMs are verified by biological experiment to involve in 22 regulations, and 14 potential eTMs are inferred by Gene Ontology enrichment analysis to involve in 63 functions, which is significant for further research.

HSP90α combined with AFP and TK1 improved the diagnostic value for hepatocellular carcinoma.

Aim: We investigated the effect of the combination of heat shock protein 90α (HSP90α), alpha-fetoprotein (AFP) and thymidine kinase 1 (TK1) in the diagnosis of hepatocellular carcinoma (HCC). Methods & results: A total of 409 patients with HCC, 101 patients with benign liver disorder and 78 healthy individuals were retrospectively analyzed. HSP90α level was higher in HCC patients than in controls. The expression of HSP90α showed a positive correlation with tumor stage, differentiation, lymph node metastasis and tumor thrombus formation. The combination of HSP90α, AFP and TK1 improved the diagnostic sensitivity (89.24%) and the area under the receiver operating characteristic curve (0.919). Conclusion: The detection of HSP90α, AFP and TK1 is more efficient than a single tumor marker for the diagnosis of HCC.

Franconibacter daqui sp. nov., a facultatively alkaliphilic species isolated from a Daqu sample.

A novel bacterium, designated strain DL503T, was isolated from a Daqu sample and its taxonomic position determined using a polyphasic taxonomy. Strain DL503T was a Gram-stain-negative, facultatively anaerobic, non-sporulating, motile and coccoid-rod-shaped bacterium. Optimum growth occurred at 20-45 °C, pH 5.0-10.0 and 1.5 % (w/v) NaCl. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the genus Franconibacter, showing highest levels of similarity with respect to Franconibacter pulveris JCM 16471T (98.94 %) and Franconibacter helveticus DSM 18396T (98.39 %). Cells contained the quinones Q-8 and MK-8, and the polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified polar lipids and three unidentified amino lipids. The DNA G+C content was 53.3 mol% and the major fatty acids were C16 : 0, C17 : 0 cyclo, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 4 (C17 : 1 iso I and/or C17 : 1 anteiso B) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The DNA-DNA relatedness values between strain DL503T and its close relatives, including F. pulveris JCM 16471T and F. helveticus DSM 18396T, were 51.5±0.5 % and 45.2±1.1 %, respectively. Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate represents a novel species of the genus Franconibacter, for which the name Franconibacter daqui sp. nov. is proposed. The type strain is DL503T (=LMG 29914T=CGMCC 1.15944T).