Combined transcriptome and proteomic analysis provides the insights into Ralstonia solanacearum pathogenicity debilitation
Ontology highlight
ABSTRACT:
ORGANISM(S): Ralstonia Solanacearum
SUBMITTER: 
Xuefang Zheng
PROVIDER: PXD081557 | iProX | Wed Jul 22 00:00:00 BST 2026
REPOSITORIES: iProX
Similar Datasets
Project description:Transcriptome sequencing is a powerful approach to globally delineate both the transcriptional and post-transcriptional genome regulation in human and other higher eukaryotes. This study sequenced the transcriptomes of two pathogenicity-differential strains of the plant wilt pathogen Verticillium dahliae. Although they showed no growth difference in vitro, hundreds of V. dahliae genes including those synthesizing aflatoxin were preferentially expressed at in the high-virulence strain. Using both the Pfam and GO annotation strategies, some of these putative virulence genes were ambiguously clustered into several known pathogenic mechanisms including hydrophobins secreted from fungal cells and acting as phytotoxin, biosynthesis of melanin protecting the fungal pathogen against host immune responses, membrane proteins of CFEM and major facilitator superfamily MFS1 with known functions in pathogenesis and multi-drug resistance, respectively. These results suggest that some pathogenicity pathways are pre-activated at the transcriptional level prior to the fungal infection of host plants. We developed two algorithms to confidently identify 1518 alternative splicing events in 1,259 Verticillium genes, representing 15.1% of multi-exonic genes. Among the events, 43.5% involving in novel splice sites were classified into nine AS types, the others belong to intron retention. Verticillium AS genes were exclusively enriched in the regulatory biological processes such as mycelium development, reproduction, morphogenesis, cell communication and signal transduction, predicting a primary function of AS regulation when the pathogen infecting its host. This work presents a transcriptome-wide approach for identifying the fungal virulence genes and pathogenicity mechanisms; both the methodology and mechanisms could be generally applicable to other fungal pathogens.
2015-04-10 | GSE45936 | GEO
Project description:Bursaphelenchus xylophilus is known as the causative agent of pine wilt disease with complex life cycles. In this research, newly published Bursaphelenchus xylophilus genome data were employed to annotate its miRNAs based on deep sequencing technologies. Four small RNA libraries derived from different infection stages of pine wilt disease were constructed and sequenced. Consequently, we obtained hundreds of evolutionarily conserved miRNAs as well as novel miRNA candidates. The analysis of miRNA expression patterns showed that most miRNAs were expressed at extraordinarily high levels during the middle stage of pine wilt disease. Subsequent stem-loop RT-PCR experiments were carried out to validate our results. Functional analysis proved that expression levels of miR-73 and miR-239 were mutually exclusive with their target GH45 cellulase genes., genes known to be responsible for the degradation of the pine cell walls. In addition, another set of atypical miRNAs, termed mirtrons, were identified from B. xylophilus introns. This discovery has expanded the current knowledgebase of such splicing-derived miRNAs into B. xylophilus. Thus, our research has provided detailed characterization of B. xylophilus miRNAs expression patterns during the pathological process of pine wilt disease. The findings will contribute to more in-depth understanding of this devastating plant disease. For the purposes of this study, we classified the pathogenic process associated with PWD into three stages in order to best characterize the expression patterns of microRNAs during the development of this devastating disease. The following describes the first stage (F): about seven days after pine trees are infected with PWNs, the tips of the pine needles begin to turn brown. Next, the middle stage (M) ensues approximately seven days later, when half of the needles on pine trees turn brown. The last stage (L) occurs another 10 days later and pine needles are complete browning. PWNs cultured on Botrytis cinerea grown on PDA medium served as the control stage (C).
2014-10-11 | E-GEOD-62255 | biostudies-arrayexpress
Project description:Background: The fungal pathogen, Fusarium oxysporum f.sp. pisi (Fop) causes fusarium wilt in peas. Races 1, 2, 5 and 6 are responsible for the majority of the economic losses globally. These are the only races present in Australia. Molecular infection mechanisms have been studied in a few other F. oxysporum formae speciales however, there has been no Fop-pea pathosystem studies. Results: A transcriptomic study was carried out to understand the molecular pathogenicity differences between the races. Transcript analysis revealed differences in the differentially expressed genes (DEGs) in the Fop races, potentially involved in fungal pathogenicity variations. Most of the DEGs in all the races were engaged in transportation, metabolism, oxidation-reduction, translation, biosynthetic processes, signal transduction, proteolysis, among others. Race 5 expressed the most virulence-associated genes. Most genes encoding for plant cell wall degrading enzymes, CAZymes and effector-like proteins were expressed in race 2. Race 6 had expressed the least number of genes during infection. Conclusion: Fop races deploy various factors and complex strategies to mitigate host defences to facilitate colonisation. This investigation provides an overview of the putative pathogenicity genes in different Fop races during infection. These genes need to be functionally characterised to confirm their pathogenicity/virulence roles and the race-specific genes can be further explored for molecular characterisation.
2020-10-22 | GSE159726 | GEO
Project description:Bursaphelenchus xylophilus is known as the causative agent of pine wilt disease with complex life cycles. In this research, newly published Bursaphelenchus xylophilus genome data were employed to annotate its miRNAs based on deep sequencing technologies. Four small RNA libraries derived from different infection stages of pine wilt disease were constructed and sequenced. Consequently, we obtained hundreds of evolutionarily conserved miRNAs as well as novel miRNA candidates. The analysis of miRNA expression patterns showed that most miRNAs were expressed at extraordinarily high levels during the middle stage of pine wilt disease. Subsequent stem-loop RT-PCR experiments were carried out to validate our results. Functional analysis proved that expression levels of miR-73 and miR-239 were mutually exclusive with their target GH45 cellulase genes., genes known to be responsible for the degradation of the pine cell walls. In addition, another set of atypical miRNAs, termed mirtrons, were identified from B. xylophilus introns. This discovery has expanded the current knowledgebase of such splicing-derived miRNAs into B. xylophilus. Thus, our research has provided detailed characterization of B. xylophilus miRNAs expression patterns during the pathological process of pine wilt disease. The findings will contribute to more in-depth understanding of this devastating plant disease.
2014-10-11 | GSE62255 | GEO
Project description:Soilborne fungal pathogens cause devastating yield losses, are highly persistent and difficult to control. To culminate infection, these organisms must cope with limited availability of iron. Here we show that the bZIP protein HapX functions as a key regulator of iron homeostasis and virulence in the vascular wilt fungus Fusarium oxysporum. Deletion of hapX does not affect iron uptake, but causes derepression of genes involved in iron-consuming pathways, leading to impaired growth under iron-depleted conditions. F. oxysporum strains lacking HapX are reduced in their capacity to invade and kill tomato plants and immunodepressed mice. The virulence defect of M-NM-^ThapX on tomato plants is exacerbated by coinoculation of roots with a biocontrol strain of Pseudomonas putida, but not with a siderophore-deficient mutant, indicating that HapX contributes to iron competition of F. oxysporum in the tomato rhizosphere. These results establish a conserved role for HapX-mediated iron homeostasis in fungal infection of plants and mammals. Iron dependent gene expression in Fusarium oxysporum wt and M-NM-^ThapX mutant was measured 1 hour after shifting the mycelia to minimal medium with or without 50 M-NM-<M Fe2(SO4)3. Three independent experiments were performed.
2012-07-13 | E-GEOD-39325 | biostudies-arrayexpress
Project description:Xanthomonas oryzae pv. oryzae (Xoo) is a rice pathogen causing bacterial blight, which outbreaks in most rice cultivating countries and reduces yield up to 50% due to no effective pesticide. Urgent responses of Xoo upon the initial contacts with rice at infection site are essential for pathogenesis. We studied the time-resolved gene expression of both transcriptome and proteome in the pathogenicity-activated Xoo cells with an in vitro assay system. Genes related to cell mobility, inorganic ion transport and effectors are early response genes to help Xoo cells invade into damaged rice leaf tissues, obtain rare cofactors, and evade rice immune responses. Although the time-resolved gene expression pattern of Xoo is conserved in both mRNA and protein, there are varied time gaps in genes between the expression peaks of mRNA and protein, which implies there is an additional translational selection step of specific mRNAs for rapid translation. The expression pattern of genes from a polycistronic mRNA in the same gene cluster is strictly conserved. The time-resolved gene expression study of Xoo in both transcriptome and proteome provides a valuable information about the pathogenic responses of Xoo at the initial stage of Xoo-rice interaction.
2021-09-09 | PXD020135 | Pride
Project description:Soilborne fungal pathogens cause devastating yield losses, are highly persistent and difficult to control. To culminate infection, these organisms must cope with limited availability of iron. Here we show that the bZIP protein HapX functions as a key regulator of iron homeostasis and virulence in the vascular wilt fungus Fusarium oxysporum. Deletion of hapX does not affect iron uptake, but causes derepression of genes involved in iron-consuming pathways, leading to impaired growth under iron-depleted conditions. F. oxysporum strains lacking HapX are reduced in their capacity to invade and kill tomato plants and immunodepressed mice. The virulence defect of ΔhapX on tomato plants is exacerbated by coinoculation of roots with a biocontrol strain of Pseudomonas putida, but not with a siderophore-deficient mutant, indicating that HapX contributes to iron competition of F. oxysporum in the tomato rhizosphere. These results establish a conserved role for HapX-mediated iron homeostasis in fungal infection of plants and mammals.
2012-07-14 | GSE39325 | GEO
Project description:Given the scarcity of known virulence factors in V. dahliae, which causes severe agricultural losses globally, identification of novel virulence genes is imperative for developing small-molecule inhibitor-based strategies against Verticillium wilt. Although gamma-glutamyl cyclotransferase (GGCT) holds promise as a therapeutic target in cancer, its functions and regulatory mechanisms in plant-pathogenic fungi remain largely elusive. In this study, we demonstrate that deletion of the VdGGCT gene severely attenuates the development and virulence of V. dahliae. Interestingly, despite belonging to the GGCT subfamily of the GGCT superfamily, VdGGCT exhibits no detectable GGCT activity towards GSH, γ-Glu-Met, or γ-Glu-Cys. Further Transcriptomic and metabolomic analyses revealed that VdGGCT is critically involved in regulating the transcription of genes and the abundance of metabolites closely associated with pathogenicity, particularly those implicated in amino acid metabolism, glutathione metabolism, and the biosynthesis of secondary metabolites. Collectively, our findings revealed the importance of VdGGCT in the development and virulence of V. dahliae, thereby identifying a novel target for the design of innovative fungicides.
2026-05-12 | GSE328568 | GEO
Project description:Running title: More insights into ovulation Purpose:Ovulation is the process by which mature follicles release fertilized oocytes under the stimulation of gonadotropin. This involves the precise interaction and destiny of various cells in the follicle. Granulosa cells (GCs) are the only cells that recognize and respond to ovulation LH (or HCG) signals. Therefore, the classification and deep interpretation of genes in GCs under LH surge stimulation is the key to understand ovulation. Methods: In this study, RNA-seq, Q-PCR, Western blot, gene knockout, gene knockout and other experimental techniques were used to conduct trend and classification analysis of the genes regulated by ovulation signal of LH at the cellular and individual levels. Genes that may be involved in ovulation were screened, identified and were selected for functional verification. Results:(1) Firstly, 7104 and 347 mRNA and Long noncoding RNA (LncRNA) that may be involved in ovulation activity were screened at the gene level by transcriptome sequencing technology, respectively. According to gene expression, they were divided into activated, inhibited and transient activated gene expression patterns. 44 secreted proteins, 62 transcription factors, 22 periodic expression characteristic genes, 10 ovulation process unknown genes, 16 LncRNA-target gene cis pair combinations and 41 highly expressed LncRNA were identified and listed in the three models;(2) The functions of LncRNA Gm12840 and Gm20186 were studied at the cellular level. The results showed that knockdown Gm12840/20186 not only inhibited the proliferation and hormone synthesis of GCs, but also induced cell apoptosis;(3) The function of LncRNA Gm12840 was further studied in mice, and Gm12840 knockout mice were constructed by CRISPR/CAS9 technology: Results It was found that Gm12840 knockout significantly increased the number of antral follicles and ovulation, and significantly inhibited the number of atretic follicles and antral follicles not discharged after ovulation. Gm12840 knockout significantly increased litter size at 2-3 months of age, but also significantly inhibited litter size at 7-9 months of age. Meanwhile, Gm12840 knockout also significantly inhibited the number of follicles growing in the ovary of 11-month-old mice;(4) Finally, transcriptomic sequencing analysis of wilt-type and Gm12840-/- mouse GCs showed 349 genes were differentially expressed. KEGG enrichment analysis and WB results showed that Gm12840 knockout enhanced mTOR and MAPK signals. Conclusions:The above results screened and identified genes with potential research value during ovulation process, and took LncRNA Gm12840 as an example to verify their functions at the cell and individual levels, providing reference for further revealing the ovulation process.
2024-08-27 | GSE182965 | GEO