scholarly journals Transcriptome Analysis of Clavibacter Michiganensis Subsp. Michiganensis-Infected Tomatoes: A Role Of Salicylic Acid In The Host Response

2021 ◽  
Author(s):  
Naoki Yokotani ◽  
Yoshinori Hasegawa ◽  
Masaru Sato ◽  
Hideki Hirakawa ◽  
Yusuke Kouzai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Salicylic Acid ◽  
Defense Response ◽  
Enrichment Analysis ◽  
Metabolic Enzyme ◽  
Clavibacter Michiganensis ◽  
Clavibacter Michiganensis Subsp ◽  
Molecular Events ◽  
Signaling Activation ◽  
Sa Signaling

Abstract Bacterial canker of tomato (Solanum lycopersicon) caused by the Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis is an economically important disease. However, the molecular events that occur are poorly understood. To understand the host defense response to C. michiganensis infection, transcriptome sequences in tomato cotyledons were analyzed by RNA-seq. Overall, 1,877 and 540 genes were upregulated and downregulated upon infection, respectively. Gene Ontology enrichment analysis revealed that genes involved in the defense response, phosphorylation, and hormone signaling were over-represented by the infection. Induced expression of defense-associated genes suggested that the tomato response to C. michiganensis showed similarities to common plant disease responses. After infection, many resistance gene analogs (RGAs) were transcriptionally upregulated, including the expressions of some receptor-like kinases (RLKs) involved in pattern-triggered immunity. The expressions of WRKYs, NACs, HSFs, and CBP60s encoding transcription factors (TFs) were upregulated, implying their involvement in defense-associated gene expression during tomato–C. michiganensis interactions. Tomato genes orthologous to Arabidopsis EDS1, EDS5/SID1, and PAD4/EDS9, which are causal genes of salicylic acid (SA)-deficient mutants, were activated, and infection drastically stimulated SA accumulation in tomatoes. Genes involved in the phenylalanine ammonia lyase pathway were upregulated, whereas metabolic enzyme gene expression in the isochorismate synthase pathway remained unchanged. Exogenously applied SA suppressed bacterial growth and induced the expression of WRKYs, suggesting that some C. michiganensis-responsive genes are regulated by SA signaling, and SA signaling activation should improve tomato immunity against C. michiganensis.

scholarly journals Transcriptome analysis of Clavibacter michiganensis subsp. michiganensis-infected tomatoes: a role of salicylic acid in the host response

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Naoki Yokotani ◽  
Yoshinori Hasegawa ◽  
Masaru Sato ◽  
Hideki Hirakawa ◽  
Yusuke Kouzai ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Defense Response ◽  
Enrichment Analysis ◽  
Metabolic Enzyme ◽  
Clavibacter Michiganensis ◽  
Clavibacter Michiganensis Subsp ◽  
Causal Genes ◽  
Host Defense Response ◽  
Signaling Activation ◽  
Sa Signaling

AbstractBacterial canker of tomato (Solanum lycopersicon) caused by the Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis (Cmm) is an economically important disease. To understand the host defense response to Cmm infection, transcriptome sequences in tomato cotyledons were analyzed by RNA-seq. Overall, 1788 and 540 genes were upregulated and downregulated upon infection, respectively. Gene Ontology enrichment analysis revealed that genes involved in the defense response, phosphorylation, and hormone signaling were over-represented by the infection. Induced expression of defense-associated genes suggested that the tomato response to Cmm showed similarities to common plant disease responses. After infection, many resistance gene analogs (RGAs) were transcriptionally upregulated, including the expressions of some receptor-like kinases (RLKs) involved in pattern-triggered immunity. The expressions of WRKYs, NACs, HSFs, and CBP60s encoding transcription factors (TFs) reported to regulate defense-associated genes were induced after infection with Cmm. Tomato genes orthologous to Arabidopsis EDS1, EDS5/SID1, and PAD4/EDS9, which are causal genes of salicylic acid (SA)-deficient mutants, were upregulated after infection with Cmm. Furthermore, Cmm infection drastically stimulated SA accumulation in tomato cotyledons. Genes involved in the phenylalanine ammonia lyase pathway were upregulated, whereas metabolic enzyme gene expression in the isochorismate synthase pathway remained unchanged. Exogenously applied SA suppressed bacterial growth and induced the expression of WRKYs, suggesting that some Cmm-responsive genes are regulated by SA signaling, and SA signaling activation should improve tomato immunity against Cmm.

scholarly journals Cyst Nematode Parasitism of Arabidopsis thaliana Is Inhibited by Salicylic Acid (SA) and Elicits Uncoupled SA-Independent Pathogenesis-Related Gene Expression in Roots

2008 ◽  
Vol 21 (4) ◽  
pp. 424-432 ◽  
Author(s):  
Martin John Evers Wubben ◽  
Jing Jin ◽  
Thomas Josef Baum
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Salicylic Acid ◽  
Plant Defense ◽  
Cyst Nematode ◽  
Wild Type ◽  
Pathogenesis Related ◽  
Nematode Parasitism ◽  
Sa Signaling ◽  
Increased Susceptibility

Compatible plant–nematode interactions involve the formation of an elaborate feeding site within the host root that requires the evasion of plant defense mechanisms by the parasite. Little is known regarding plant defense signaling pathways that limit nematode parasitism during a compatible interaction. Therefore, we utilized Arabidopsis thaliana mutants perturbed in salicylic acid (SA) biosynthesis or signal transduction to investigate the role of SA in inhibiting parasitism by the beet cyst nematode Heterodera schachtii. We determined that SA-deficient mutants (sid2-1, pad4-1, and NahG) exhibited increased susceptibility to H. schachtii. In contrast, SA-treated wild-type plants showed decreased H. schachtii susceptibility. The npr1-2 and npr1-3 mutants, which are impaired in SA signaling, also showed increased susceptibility to H. schachtii, whereas the npr1-suppressor mutation sni1 showed decreased susceptibility. Constitutive pathogenesis-related (PR) gene-expressing mutants (cpr1 and cpr6) did not show altered susceptibility to H. schachtii; however, constitutive PR gene expression was restricted to cpr1 shoots with wild-type levels of PR-1 transcript present in cpr1 roots. Furthermore, we determined that H. schachtii infection elicits SA-independent PR-2 and PR-5 induction in wild-type roots, while PR-1 transcript and total SA levels remained unaltered. This was in contrast to shoots of infected plants where PR-1 transcript abundance and total SA levels were elevated. We conclude that SA acts via NPR1 to inhibit nematode parasitism which, in turn, is negatively regulated by SNI1. Our results show an inverse correlation between root basal PR-1 expression and plant susceptibility to H. schachtii and suggest that successful cyst nematode parasitism may involve a local suppression of SA signaling in roots.

Gene Expression Analysis during Interaction of Tomato and Related Wild Species with Clavibacter michiganensis subsp. michiganensis

2011 ◽  
Vol 30 (2) ◽  
pp. 498-511 ◽  
Author(s):  
José Pablo Lara-Ávila ◽  
María Isabel Isordia-Jasso ◽  
Rosalba Castillo-Collazo ◽  
June Simpson ◽  
Ángel Gabriel Alpuche-Solís
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Wild Species ◽  
Gene Expression Analysis ◽  
Clavibacter Michiganensis ◽  
Clavibacter Michiganensis Subsp ◽  
Related Wild Species

scholarly journals Silencing of Host Basal Defense Response-Related Gene Expression Increases Susceptibility of Nicotiana benthamiana to Clavibacter michiganensis subsp. michiganensis

2011 ◽  
Vol 101 (3) ◽  
pp. 349-357 ◽  
Author(s):  
Vasudevan Balaji ◽  
Guido Sessa ◽  
Christine D. Smart
Keyword(s):  
Defense Response ◽  
Nicotiana Benthamiana ◽  
Plant Responses ◽  
Virus Induced Gene Silencing ◽  
In Planta ◽  
Clavibacter Michiganensis ◽  
Canker Disease ◽  
Clavibacter Michiganensis Subsp ◽  
Genes Encoding ◽  
Basal Defense

Clavibacter michiganensis subsp. michiganensis is an actinomycete, causing bacterial wilt and canker disease of tomato (Solanum lycopersicum). We used virus-induced gene silencing (VIGS) to identify genes playing a role in host basal defense response to C. michiganensis subsp. michiganensis infection using Nicotiana benthamiana as a model plant. A preliminary VIGS screen comprising 160 genes from tomato known to be involved in defense-related signaling identified a set of 14 genes whose suppression led to altered host–pathogen interactions. Expression of each of these genes and three additional targets was then suppressed in larger-scale VIGS experiments and the effect of silencing on development of wilt disease symptoms and bacterial growth during an N. benthamiana–C. michiganensis subsp. michiganensis compatible interaction was determined. Disease susceptibility and in planta bacterial population size were enhanced by silencing genes encoding N. benthamiana homologs of ubiquitin activating enzyme, snakin-2, extensin-like protein, divinyl ether synthase, 3-hydroxy-3-methylglutaryl-coenzyme A reductase 2, and Pto-like kinase. The identification of genes having a role in the host basal defense-response to C. michiganensis subsp. michiganensis advances our understanding of the plant responses activated by C. michiganensis subsp. michiganensis and raises possibilities for devising novel and effective molecular strategies to control bacterial canker and wilt in tomato.

scholarly journals Electrical Stimulation Enhances Plant Defense Response in Grapevine through Salicylic Acid-Dependent Defense Pathway

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1316
Author(s):  
Daisuke Mori ◽  
Ayane Moriyama ◽  
Hiroshi Kanamaru ◽  
Yoshinao Aoki ◽  
Yoshiyuki Masumura ◽  
...  
Keyword(s):  
Gene Expression ◽  
Salicylic Acid ◽  
Electrical Stimulation ◽  
Plant Defense ◽  
Pest Management ◽  
Defense Response ◽  
Management Strategies ◽  
Gray Mold ◽  
Plant Defense Response ◽  
Abiotic Elicitor

Concern over environmental pollution generated by chemical fungicides has led to the introduction of alternative pest management strategies to chemical fungicide application. One of those strategies is the induction of plant defense response by an abiotic elicitor. In the present study, field-grown grapevines were subjected to electrical stimulation using a solar panel from two weeks before flowering to harvest in the 2016 and 2020 growing seasons. In both years, electrical stimulation decreased the incidence of gray mold and/or ripe rot on bunches and downy mildew on leaves of the field-grown grapevine. Transcription of a gene encoding β-1,3-glucanase but not class IV chitinase in leaves of potted grapevine seedlings was upregulated 20 days after electrical stimulation, suggesting that electrical stimulation acts as an abiotic elicitor of plant defense response to fungal diseases. The gene expression of PR1 but not PDF1.2 was upregulated in Arabidopsis plants subjected to electrical stimulation. On the other hand, PR1 gene expression was not induced in salicylic acid (SA)-insensitive Arabidopsis mutant npr1-5 subjected to electrical stimulation. Taken together, electrical stimulation is responsible for plant defense response through the SA-dependent defense pathway. These findings would help us develop a novel and innovative practical technique that uses electrical stimulation in integrated pest management.

A Method of Pathway Enrichment Analysis Based Gene Expression Variability

2013 ◽  
Vol 40 (12) ◽  
pp. 1256
Author(s):  
XiaoDong JIA ◽  
XiuJie CHEN ◽  
Xin WU ◽  
JianKai XU ◽  
FuJian TAN ◽  
...  
Keyword(s):  
Gene Expression ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Expression Variability ◽  
Pathway Enrichment

scholarly journals Identification of potential biomarkers for abdominal pain in IBS patients by bioinformatics approach

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhongyuan Lin ◽  
Yimin Wang ◽  
Shiqing Lin ◽  
Decheng Liu ◽  
Guohui Mo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Irritable Bowel Syndrome ◽  
Abdominal Pain ◽  
Gastrointestinal Disease ◽  
Rectal Mucosa ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Irritable Bowel ◽  
Potential Biomarkers

Abstract Background Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disease characterized by chronic abdominal discomfort and pain. The mechanisms of abdominal pain, as a relevant symptom, in IBS are still unclear. We aimed to explore the key genes and neurobiological changes specially involved in abdominal pain in IBS. Methods Gene expression data (GSE36701) was downloaded from Gene Expression Omnibus database. Fifty-three rectal mucosa samples from 27 irritable bowel syndrome with diarrhea (IBS-D) patients and 40 samples from 21 healthy volunteers as controls were included. Differentially expressed genes (DEGs) between two groups were identified using the GEO2R online tool. Functional enrichment analysis of DEGs was performed on the DAVID database. Then a protein–protein interaction network was constructed and visualized using STRING database and Cytoscape. Results The microarray analysis demonstrated a subset of genes (CCKBR, CCL13, ACPP, BDKRB2, GRPR, SLC1A2, NPFF, P2RX4, TRPA1, CCKBR, TLX2, MRGPRX3, PAX2, CXCR1) specially involved in pain transmission. Among these genes, we identified GRPR, NPFF and TRPA1 genes as potential biomarkers for irritating abdominal pain of IBS patients. Conclusions Overexpression of certain pain-related genes (GRPR, NPFF and TRPA1) may contribute to chronic visceral hypersensitivity, therefore be partly responsible for recurrent abdominal pain or discomfort in IBS patients. Several synapses modification and biological process of psychological distress may be risk factors of IBS.

Root exposure to apple replant disease soil triggers local defense response and rhizoplane microbiome dysbiosis

2021 ◽  
Author(s):  
Alicia Balbín-Suárez ◽  
Samuel Jacquiod ◽  
Annmarie-Deetja Rohr ◽  
Benye Liu ◽  
Henryk Flachowsky ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Defense ◽  
Defense Response ◽  
Soil Column ◽  
Soil Layer ◽  
Soil Microbiome ◽  
Control Soil ◽  
Apple Rootstocks ◽  
Apple Replant Disease ◽  
Replant Disease

Abstract A soil column split-root experiment was designed to investigate the ability of apple replant disease (ARD) causing agents to spread in soil. ‘M26’ apple rootstocks grew into a top layer of Control soil, followed by a barrier-free split-soil layer (Control soil/ARD soil). We observed a severely reduced root growth, concomitant with enhanced gene expression of phytoalexin biosynthetic genes and phytoalexin content in roots from ARD soil, indicating a pronounced local plant defense response. Amplicon sequencing (bacteria, archaea, fungi) revealed local shifts in diversity and composition of microorganisms in the rhizoplane of roots from ARD soil. An enrichment of OTUs affiliated to potential ARD fungal pathogens (Ilyonectria and Nectria sp.) and bacteria frequently associated with ARD (Streptomyces, Variovorax) was noted. In conclusion, our integrated study supports the idea of ARD being local and not spreading into surrounding soil, as only the roots in ARD soil were affected in terms of growth, phytoalexin biosynthetic gene expression, phytoalexin production, and altered microbiome structure. This study further reinforces the microbiological nature of ARD, being likely triggered by a disturbed soil microbiome enriched with low mobility ARD-causing agents that induce a strong plant defense and rhizoplane microbiome dysbiosis, concurring with root damage.

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