ceRNA Cross-Talk in Paulownia Witches' Broom Disease

Integrating multiregulatory analysis reveals the negative regulatory function of miR482a in the response of poplar to canker pathogen infection

Canker disease caused by the bacterium Lonsdalea populi is one of the most destructive diseases affecting poplar stems. However, the detailed stress response mechanisms of poplar have not been widely characterized. To explore the diverse regulatory RNA landscape and the function of key regulators in poplar subjected to L. populi stress, we integrated time-course experiment with mock-inoculation (CK) and inoculation (IN) with L. populi at the first, third, and sixth day (IN1, IN3, IN6) on Populus × euramericana cv. '74/76' (107), small RNA-seq, whole transcriptome-wide analysis, degradome analysis and transgenic experiments. A total of 98 differentially expressed (DE) miRNA, 17 974 DEmRNA, and 807 DElncRNA were identified in poplar infected by L. populi, presenting dynamic changes over the infection course. Regulatory networks among RNAs were further constructed. Notably, a network centered on ptc-miR482a in CK-vs-IN3 contained most DEGs. We show that miR482a and miR1448 are located in one transcript as a polycistron. Overexpression of pre-miR482a-miR1448 (OX482-1448) and pre-miR482a (OX482) increased poplar susceptibility to canker pathogen with reduced accumulation of reactive oxygen species, while the suppression of miR482a (STTM482) conferred poplar disease resistance. PHA7 was validated as the target of miR482a with degradome sequencing and tobacco transient co-transformation, its expression being downregulated in OX482-1448 and OX482 lines. Additionally, a series of phasiRNAs were triggered by miR482a targeting PHA7, forming regulatory cascades with more RLP, NBS-LRR, and PK genes, further verifying the defense function of miR482a. These findings provide insights for understanding the roles of ncRNAs and regulatory networks involved in poplar immunity.

Novel Insight into the Prevention and Therapeutic Treatment of Paulownia Witches' Broom: A Study on the Effect of Salicylic Acid on Disease Control and the Changes in the Paulownia Transcriptome and Proteome

Paulownia species not only have significant economic benefits but also show great potential in ecological conservation. However, they are highly susceptible to phytoplasma infections, causing Paulownia witches' broom (PaWB), which severely restricts the development of the Paulownia industry. Salicylic acid (SA) plays a crucial role in plant disease resistance. However, there have been no reports on the effect of SA on PaWB. Due to the properties of SA, it may have potential in controlling PaWB. Based on the above speculation, the prevention and therapeutic effect of SA on PaWB and its effect on the PaWB-infected Paulownia transcriptome and proteome were studied in this work. The results indicated that 0.1 mmol/L was the optimal SA concentration for inhibiting the germination of Paulownia axillary buds. In terms of resistance physiological indicators, SA treatment significantly affected both Paulownia tomentosa infected (PTI) seedlings and Paulownia fortunei infected (PFI) seedlings, where the activities of peroxidase (POD) and superoxide dismutase (SOD) were enhanced. Malondialdehyde (MDA), O2-, and H2O2, however, were significantly reduced. Specifically, after SA treatment, SOD activity increased by 28% in PFI and 25% in PTI, and POD activity significantly increased by 61% in PFI and 58% in PTI. Moreover, the MDA content decreased by 30% in PFI and 23% in PTI, the H2O2 content decreased by 26% in PFI and 19% in PTI, and the O2- content decreased by 21% in PFI and 19% in PTI. Transcriptomic analysis showed that there were significant upregulations of MYB, NAC, and bHLH and other transcription factors after SA treatment. Moreover, genes involved in PaWB-related defense responses such as RAX2 also showed significant differences. Furthermore, proteomic analysis indicated that after SA treatment, proteins involved in signal transduction, protein synthesis modification, and disease defense were differentially expressed. This work provides a research foundation for the prevention and treatment of PaWB and offers references for exploring anti-PaWB methods.

Paulownia Witches' Broom Disease: A Comprehensive Review

Phytoplasmas are insect-transmitted bacterial pathogens associated with diseases in a wide range of host plants, resulting in significant economic and ecological losses. Perennial deciduous trees in the genus Paulownia are widely planted for wood harvesting and ornamental purposes. Paulownia witches' broom (PaWB) disease, associated with a 16SrI-D subgroup phytoplasma, is a destructive disease of paulownia in East Asia. The PaWB phytoplasmas are mainly transmitted by insect vectors in the Pentatomidae (stink bugs), Miridae (mirid bugs) and Cicadellidae (leafhoppers) families. Diseased trees show typical symptoms, such as branch and shoot proliferation, which together are referred to as witches' broom. The phytoplasma presence affects the physiological and anatomical structures of paulownia. Gene expression in paulownia responding to phytoplasma presence have been studied at the transcriptional, post-transcriptional, translational and post-translational levels by high throughput sequencing techniques. A PaWB pathogenic mechanism frame diagram on molecular level is summarized. Studies on the interactions among the phytoplasma, the insect vectors and the plant host, including the mechanisms underlying how paulownia effectors modify processes of gene expression, will lead to a deeper understanding of the pathogenic mechanisms and to the development of efficient control measures.

Current perspectives of lncRNAs in abiotic and biotic stress tolerance in plants

Abiotic/biotic stresses pose a major threat to agriculture and food security by impacting plant growth, productivity and quality. The discovery of extensive transcription of large RNA transcripts that do not code for proteins, termed long non-coding RNAs (lncRNAs) with sizes larger than 200 nucleotides in length, provides an important new perspective on the centrality of RNA in gene regulation. In plants, lncRNAs are widespread and fulfill multiple biological functions in stress response. In this paper, the research advances on the biological function of lncRNA in plant stress response were summarized, like as Natural Antisense Transcripts (NATs), Competing Endogenous RNAs (ceRNAs) and Chromatin Modification etc. And in plants, lncRNAs act as a key regulatory hub of several phytohormone pathways, integrating abscisic acid (ABA), jasmonate (JA), salicylic acid (SA) and redox signaling in response to many abiotic/biotic stresses. Moreover, conserved sequence motifs and structural motifs enriched within stress-responsive lncRNAs may also be responsible for the stress-responsive functions of lncRNAs, it will provide a new focus and strategy for lncRNA research. Taken together, we highlight the unique role of lncRNAs in integrating plant response to adverse environmental conditions with different aspects of plant growth and development. We envisage that an improved understanding of the mechanisms by which lncRNAs regulate plant stress response may further promote the development of unconventional approaches for breeding stress-resistant crops.

Bioinformatic Analysis of the BTB Gene Family in Paulownia fortunei and Functional Characterization in Response to Abiotic and Biotic Stresses

To learn about the gene structure, phylogenetic evolution, and function under biotic and abiotic stresses of BTB (Bric-a-Brac/Tramtrack/Broad Complex) genes in Paulownia fortunei, a whole-genome sequence evaluation was carried out, and a total of 62 PfBTB genes were identified. The phylogenetic analysis showed that PfBTB proteins are divided into eight groups, and these proteins are highly conserved. PfBTB genes were unevenly distributed on 17 chromosomes. The colinearity analysis found that fragment replication and tandem replication are the main modes of gene amplification in the PfBTB family. The analysis of cis-acting elements suggests that PfBTB genes may be involved in a variety of biological processes. The transcriptomic analysis results showed that PfBTB3/12/14/16/19/36/44 responded to Paulownia witches' broom (PaWB), while PfBTB1/4/17/43 responded to drought stress, and the RT-qPCR results further support the reliability of transcriptome data. In addition, the association analysis between miRNA and transcriptome revealed a 91-pair targeting relationship between miRNAs and PfBTBs. In conclusion, the BTB genes in Paulownia are systematically identified in this research. This work provides useful knowledge to more fully appreciate the potential functions of these genes and their possible roles in the occurrence of PaWB and in response to stress.

The stability of transcription factor PfSPL1 participates in the response to phytoplasma stress in Paulownia fortunei

The current understanding of the pathogenesis of phytoplasma is still very limited and challenging. Here, ceRNA regulatory network and degradome sequencing identified a PfmiR156f-PfSPL regulatory module in Paulownia fortunei infected by phytoplasma, and RLM-5'RACE and dual luciferase analyses verified the relationship. The PfmiR156 cleavage site was located at 1104 nt and 1177 nt of PfSPL1 and PfSPL10, respectively. MG132 and epoxomicin, two 26S proteasome inhibitors, significantly increased the accumulation of PfSPL1. PfSPL1 was also the attack target of phytoplasma effectors (Pawb 3/9/16/37/51) after the phytoplasma invaded Paulownia. Moreover, molecular docking implied that the effectors may interact with the conserved SBP domain of the target protein PfSPL1. Basically, these results indicated that the stability of PfSPL1 was regulated by PfmiR156 cleavage activity and/or the 26S proteasome pathway at the post-translation level. The PfSPL1, which is a transcription factor, was also the one of the targets of multiple effectors attacking Paulownia. This study provides a good scope to understand the paulownia phytoplasma infecting mechanism.

Genome-Wide Identification and Expression of the Paulownia fortunei MADS-Box Gene Family in Response to Phytoplasma Infection

Paulownia witches’ broom (PaWB), caused by phytoplasmas, is the most devastating infectious disease of Paulownia. Although a few MADS-box transcription factors have been reported to be involved in the formation of PaWB, there has been little investigation into all of the MADS-box gene family in Paulownia. The objective of this study is to identify the MADS-box gene family in Paulownia fortunei on a genome-wide scale and explore their response to PaWB infection. Bioinformatics software were used for identification, characterization, subcellular localization, phylogenetic analysis, the prediction of conserved motifs, gene structures, cis-elements, and protein-protein interaction network construction. The tissue expression profiling of PfMADS-box genes was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Transcriptome data and the protein interaction network prediction were combined to screen the genes associated with PaWB formation. We identified 89 MADS-box genes in the P. fortunei genome and categorized them into 14 subfamilies. The comprehensive analysis showed that segment duplication events had significant effects on the evolution of the PfMADS-box gene family; the motif distribution of proteins in the same subfamily are similar; development-related, phytohormone-responsive, and stress-related cis-elements were enriched in the promoter regions. The tissue expression pattern of PfMADS-box genes suggested that they underwent subfunctional differentiation. Three genes, PfMADS3, PfMADS57, and PfMADS87, might be related to the occurrence of PaWB. These results will provide a valuable resource to explore the potential functions of PfMADS-box genes and lay a solid foundation for understanding the roles of PfMADS-box genes in paulownia–phytoplasma interactions.

Role of long non coding RNA in plants under abiotic and biotic stresses

Evolutionary processes have evolved plants to cope with several different natural stresses. Basic physiological activities of crop plants are significantly harmed by these stresses, reducing productivity and eventually leading to death. The recent advancements in high-throughput sequencing of transcriptome and expression profiling with NGS techniques lead to the innovation of various RNAs which do not code for proteins, more specifically long non-coding RNAs (lncRNAs), undergirding regulate growth, development, and the plant defence mechanism transcriptionally under stress situations. LncRNAs are a diverse set of RNAs that play key roles in various biological processes at the level of transcription, post-transcription, and epigenetics. These are thought to serve crucial functions in plant immunity and response to changes in the environment. In plants, however, just a few lncRNAs have been functionally identified. In this review, we will address recent advancements in comprehending lncRNA regulatory functions, focusing on the expanding involvement of lncRNAs in modulating environmental stress responsiveness in plants.

Whole-transcriptome analyses of Sorghum leaves identify key mRNAs and ncRNAs associated with GA3-mediated alleviation of salt stress

Sorghum has recently attracted much attention for its tolerance in high salt environment. However, the effect and regulatory mechanism of the gibberellic acid (GA₃)-mediated alleviation of salt stress in sorghum remains unclear. Herein, we reported that a GA₃ concentration of 50 mg/L is optimal for sorghum ("Jitian 3") development under salt stress. We conducted a whole-transcriptome analysis between GA₃-treated and control sorghum leaves under salt stress, and we identified 1002 differentially expressed (DE)-messenger RNAs (mRNAs), 81 DE-long non-coding RNAs (lncRNAs), 7 DE-circular RNAs (circRNAs), and 26 DE-microRNA (miRNAs) in sorghum following GA₃ treatment. We also identified a majority of DE-mRNAs and non-coding RNAs (ncRNAs) targets that serve essential roles in phenylpropanoid biosynthesis and plant hormone networks. In addition, we generated a competitive endogenous RNA (ceRNA)-miRNA-target gene network, and 3 circRNAs (circRNA_2746, circRNA_6515, circRNA_5622), 4 lncRNAs (XR_002450182.1, XR_002452422.1, XR_002448510.1, XR_002448296.1) and 4 genes (LOC8056546, LOC8062245, LOC8061469, LOC8071960) probably act as valuable candidates for the regulation of the GA₃-mediated alleviation of salt stress in sorghum. Our findings uncovered potential mRNA and non-coding RNAs that contribute to GA₃ regulation, thus offering a basis for the future investigation of underlying mechanisms of salt stress in sorghum.

Whole-transcriptome analysis and construction of an anther development-related ceRNA network in Chinese cabbage (Brassica campestris L. ssp. pekinensis)

Anther development is precisely regulated by a complex gene network, which is of great significance to plant breeding. However, the molecular mechanism of anther development in Chinese cabbage is unclear. Here, we identified microRNAs (miRNAs), mRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to anther development in Chinese cabbage (Brassica campestris L. ssp. pekinensis) to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge on anther development. Using whole-transcriptome sequencing, 9055, 585, 1344, and 165 differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), lncRNAs (DElncRNAs), and circRNAs (DEcircRNAs) were identified, respectively, in the anthers of Chinese cabbage compared with those in samples of the vegetative mass of four true leaves. An anther-related ceRNA regulatory network was constructed using miRNA targeting relationships, and 450 pairs of ceRNA relationships, including 97 DEmiRNA-DEmRNA, 281 DEmiRNA-DElncRNA, and 23 DEmiRNA-DEcircRNA interactions, were obtained. We identified important genes and their interactions with lncRNAs, circRNAs, and miRNAs involved in microsporogenesis, tapetum and callose layer development, pollen wall formation, and anther dehiscence. We analyzed the promoter activity of six predominant anther expression genes, which were expressed specifically in the anthers of Arabidopsis thaliana, indicating that they may play an important role in anther development of Chinese cabbage. This study lays the foundation for further research on the molecular mechanisms of anther growth and development in Chinese cabbage.

Conformational Changes in Three-Dimensional Chromatin Structure in Paulownia fortunei After Phytoplasma Infection

Higher-order chromatin structures play important roles in regulating multiple biological processes such as growth and development as well as biotic and abiotic stress response. However, little is known about three-dimensional chromatin structures in Paulownia or about whole-genome chromatin conformational changes that occur in response to Paulownia witches' broom (PaWB) disease. We used high-throughput chromosome conformation capture (Hi-C) to obtain genome-wide profiles of chromatin conformation in both healthy and phytoplasma-infected Paulownia fortunei genome. The heat map results indicated that the strongest interactions between chromosomes were in the telomeres. We confirmed that the main structural characteristics of A/B compartments, topologically associated domains, and chromatin loops were prominent in the Paulownia genome and were clearly altered in phytoplasma-infected plants. By combining chromatin immunoprecipitation sequencing, Hi-C signals, and RNA sequencing data, we inferred that the chromatin structure changed and the modification levels of three histones (H3K4me3/K9ac/K36me3) increased in phytoplasma-infected P. fortunei, which was associated with changes of transcriptional activity. We concluded that for epigenetic modifications, transcriptional activity might function in combination to shape chromatin packing in healthy and phytoplasm-infected Paulownia. Finally, 11 genes (e.g., RPN6, Sec61 subunit-α) that were commonly located at specific topologically associated domain boundaries, A/B compartment switching and specific loops, and had been associated with histone marks were identified and considered as closely related to PaWB stress. Our results provide new insights into the nexus between gene regulation and chromatin conformational alterations in nonmodel plants upon phytopathogen infection and plant disease resistance.

Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis)

BACKGROUND

The transition from vegetative growth to reproductive growth involves various pathways. Vernalization is a crucial process for floral organ formation and regulation of flowering time that is widely utilized in plant breeding. In this study, we aimed to identify the global landscape of mRNAs, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to vernalization in Chinese cabbage. These data were then used to construct a competitive endogenous RNA (ceRNA) network that provides valuable information to better understand the vernalization response.

RESULTS

In this study, seeds sampled from the Chinese cabbage doubled haploid (DH) line 'FT' with or without vernalization treatment were used for whole-transcriptome sequencing. A total of 2702 differentially expressed (DE) mRNAs, 151 DE lncRNAs, 16 DE circRNAs, and 233 DE miRNAs were identified in the vernalization-treated seeds. Various transcription factors, such as WRKY, MYB, NAC, bHLH, MADS-box, zinc finger protein CONSTANS-like gene, and B3 domain protein, and regulatory proteins that play important roles in the vernalization pathway were identified. Additionally, we constructed a vernalization-related ceRNA-miRNA-target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA‒DEmRNA, 67 DEmiRNA‒DElncRNA, and 12 DEmiRNA‒DEcircRNA interactions, in Chinese cabbage. Furthermore, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs, which are involved in the regulation of flowering time, floral organ formation, bolting, and flowering, were identified.

CONCLUSIONS

Our results reveal the potential mRNA and non-coding RNAs involved in vernalization, providing a foundation for further studies on the molecular mechanisms underlying vernalization in Chinese cabbage.

Review: Biological functions of major latex-like proteins in plants

Major latex-like proteins (MLPs) have been identified in dicots and monocots. They are members of the birch pollen allergen Bet v 1 family as well as pathogenesis-related proteins class 10. MLPs have two main features. One is binding affinity toward various hydrophobic compounds, such as long-chain fatty acids, steroids, and systemic acquired resistance signals, via its internal hydrophobic cavity or hydrophobic residues on its surface. MLPs transport such compounds to other organs via phloem and xylem vessels and contribute to the expression of physiologically important ligands' activity in the particular organs. The second feature is responses to abiotic and biotic stresses. MLPs are involved in drought and salt tolerance through the mediation of plant hormone signaling pathways. MLPs generate resistance against pathogens by the induction of pathogenesis-related protein genes. Therefore, MLPs play crucial roles in drought and salt tolerance and resistance against pathogens. However, knowledge of MLPs is fragmented, and an overview of them is needed. Herein, we summarize the current knowledge of the biological functions of MLPs, which to our knowledge, is the first review about MLPs that has been reported.