scholarly journals Evaluation of small non-coding RNAs as a possible epigenetic mechanism mediating the transition from biotrophy to necrotrophy in the life cycle of Phytophthora infestans

2021 ◽  
Author(s):  
Juliana Gonzalez-Tobon ◽  
Alejandra Rodriguez-Jaramillo ◽  
Laura Milena Forero ◽  
Laura Natalia Gonzalez ◽  
Giovanna Danies-Turano ◽  
...  
Keyword(s):  
Life Cycle ◽  
Phytophthora Infestans ◽  
Epigenetic Mechanism ◽  
Functional Categories ◽  
First Feeding ◽  
Starting Point ◽  
Genes Encoding ◽  
Role Players ◽  
Non Coding Rnas ◽  
Blight Disease

Phytophthora infestans, causal agent of late blight disease of potatoes, causes billion-dollar losses worldwide each year. This plant pathogen is a hemibiotroph, first feeding on the host and later killing it. Even though the transcription dynamics of this transition are characterized, the role that small non-coding RNAs (sRNAs) might have is still unknown. Furthermore, a bioinformatic pipeline to search and analyze sRNAs in P. infestans, is needed. Using our proposed pipeline, 146 sRNAs were found to be significantly differentially expressed between the evaluated stages of the pathogens life cycle. One hundred of these sRNAs were successfully annotated and classified into nine functional categories. The expression of the genes associated to ten of these sRNAs was validated via qRT-PCR. Among these, the expression levels of genes encoding for effectors were inversely correlated to that of the sRNAs aligning to them, which is expected if sRNAs are indeed regulating their expression. This correlation was not clear for sRNAs in other functional categories and should not be confused with strict causality. This study works as a starting point for considering sRNAs as role players in the transition from biotrophy to necrotrophy in P. infestans when infecting Solanum tuberosum.

Evaluation of small ncRNAs as a possible epigenetic mechanism mediating the transition from biotrophy to necrotrophy in the life cycle of Phytophthora infestans

2019 ◽  
Author(s):  
Juliana Gonzalez-Tobon ◽  
Alejandra Rodriguez-Jaramillo ◽  
Laura Milena Forero ◽  
Laura Natalia González ◽  
Giovanna Danies ◽  
...  
Keyword(s):  
Life Cycle ◽  
Phytophthora Infestans ◽  
Effector Proteins ◽  
Epigenetic Mechanism ◽  
Data Sets ◽  
Small Noncoding Rnas ◽  
Regulatory Processes ◽  
Small Ncrnas ◽  
Blight Disease ◽  
Efficient Option

Abstract Background: Phytophthora infestans, the causal agent of late blight disease of potato and tomato, is responsible for billions of dollars in losses worldwide each year. This plant pathogen is a hemibiotroph, meaning that in the early stages of infection, it feeds on living host tissue, and later in the infection cycle, it kills the host. Even though the transcription dynamics of this transition are well characterized, information on the role of small noncoding RNAs (ncRNAs) during this process is still being obtained. Furthermore, a methodological pipeline useful for searching and analyzing small ncRNAs in this pathogen is needed. Results: Using the proposed pipeline, a set of 146 small ncRNAs were found to be significantly differentially expressed among the analyzed samples. From these, 100 small ncRNAs were successfully annotated to specific genes, some of them encoding effector proteins produced by the pathogen during its life cycle. Other molecular regulatory processes, mainly mediated by enzymes and transporters, were also identified. Conclusions: The pipeline presented here is an easy-to-use, comprehensive and efficient option for analyzing small ncRNA profiles of P. infestans small RNA-seq data sets. Additionally, the results presented here may further contribute to elucidating the specific molecular and epigenetic mechanisms controlling the life cycle of P. infestans.

scholarly journals Evaluation of small ncRNAs as a possible epigenetic mechanism mediating the transition from biotrophy to necrotrophy in the life cycle of Phytophthora infestans

2019 ◽  
Author(s):  
Juliana Gonzalez-Tobon ◽  
Alejandra Rodriguez-Jaramillo ◽  
Laura Milena Forero ◽  
Laura Natalia González ◽  
Giovanna Danies ◽  
...  
Keyword(s):  
Life Cycle ◽  
Phytophthora Infestans ◽  
Effector Proteins ◽  
Epigenetic Mechanism ◽  
Data Sets ◽  
Small Noncoding Rnas ◽  
Regulatory Processes ◽  
Small Ncrnas ◽  
Blight Disease ◽  
Efficient Option

Abstract Background Phytophthora infestans, the causal agent of late blight disease of potato and tomato, is responsible for billions of dollars in losses worldwide each year. This plant pathogen is a hemibiotroph, meaning that in the early stages of infection, it feeds on living host tissue, and later in the infection cycle, it kills the host. Even though the transcription dynamics of this transition are well characterized, information on the role of small noncoding RNAs (ncRNAs) during this process is still being obtained. Furthermore, a methodological pipeline useful for searching and analyzing small ncRNAs in this pathogen is needed. Results Using the proposed pipeline, a set of 146 small ncRNAs were found to be significantly differentially expressed among the analyzed samples. From these, 100 small ncRNAs were successfully annotated to specific genes, some of them encoding effector proteins produced by the pathogen during its life cycle. Other molecular regulatory processes, mainly mediated by enzymes and transporters, were also identified. Conclusions The pipeline presented here is an easy-to-use, comprehensive and efficient option for analyzing small ncRNA profiles of P. infestans small RNA-seq data sets. Additionally, the results presented here may further contribute to elucidating the specific molecular and epigenetic mechanisms controlling the life cycle of P. infestans.

scholarly journals The Impact of Steroidal Glycoalkaloids on the Physiology of Phytophthora infestans, the Causative Agent of Potato Late Blight

2017 ◽  
Vol 30 (7) ◽  
pp. 531-542 ◽  
Author(s):  
Paul Dahlin ◽  
Marion C. Müller ◽  
Sophia Ekengren ◽  
Lauren S. McKee ◽  
Vincent Bulone
Keyword(s):  
Late Blight ◽  
Phytophthora Infestans ◽  
Causative Agent ◽  
Management Strategies ◽  
Plant Secondary Metabolites ◽  
Glycoside Hydrolases ◽  
Genes Encoding ◽  
Phytopathogenic Microorganisms ◽  
Blight Disease ◽  
The Impact

Steroidal glycoalkaloids (SGAs) are plant secondary metabolites known to be toxic to animals and humans and that have putative roles in defense against pests. The proposed mechanisms of SGA toxicity are sterol-mediated disruption of membranes and inhibition of cholinesterase activity in neurons. It has been suggested that phytopathogenic microorganisms can overcome SGA toxicity by enzymatic deglycosylation of SGAs. Here, we have explored SGA-mediated toxicity toward the invasive oomycete Phytophthora infestans, the causative agent of the late blight disease in potato and tomato, as well as the potential for SGA deglycosylation by this species. Our growth studies indicate that solanidine, the nonglycosylated precursor of the potato SGAs α-chaconine and α-solanine, has a greater physiological impact than its glycosylated forms. All of these compounds were incorporated into the mycelium, but only solanidine could strongly inhibit the growth of P. infestans in liquid culture. Genes encoding several glycoside hydrolases with potential activity on SGAs were identified in the genome of P. infestans and were shown to be expressed. However, we found no indication that deglycosylation of SGAs takes place. We present additional evidence for apparent host-specific adaptation to potato SGAs and assess all results in terms of future pathogen management strategies.

scholarly journals Divergence in Coding Sequence and Expression of Different Functional Categories of Immune Genes between Two Wild Rodent Species

2021 ◽  
Vol 13 (3) ◽  
Author(s):  
Xiuqin Zhong ◽  
Max Lundberg ◽  
Lars Råberg
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Immune Function ◽  
Sequence Divergence ◽  
Expression Divergence ◽  
Functional Categories ◽  
Coding Sequence ◽  
Immune Genes ◽  
Genes Encoding ◽  
Signal Transduction Proteins

Abstract Differences in immune function between species could be a result of interspecific divergence in coding sequence and/or expression of immune genes. Here, we investigate how the degree of divergence in coding sequence and expression differs between functional categories of immune genes, and if differences between categories occur independently of other factors (expression level, pleiotropy). To this end, we compared spleen transcriptomes of wild-caught yellow-necked mice and bank voles. Immune genes expressed in the spleen were divided into four categories depending on the function of the encoded protein: pattern recognition receptors (PRR); signal transduction proteins; transcription factors; and cyto- and chemokines and their receptors. Genes encoding PRR and cyto-/chemokines had higher sequence divergence than genes encoding signal transduction proteins and transcription factors, even when controlling for potentially confounding factors. Genes encoding PRR also had higher expression divergence than genes encoding signal transduction proteins and transcription factors. There was a positive correlation between expression divergence and coding sequence divergence, in particular for PRR genes. We propose that this is a result of that divergence in PRR coding sequence leads to divergence in PRR expression through positive feedback of PRR ligand binding on PRR expression. When controlling for sequence divergence, expression divergence of PRR genes did not differ from other categories. Taken together, the results indicate that coding sequence divergence of PRR genes is a major cause of differences in immune function between species.

scholarly journals Analysis of saponins detoxification genes in Ilyonectria mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

2021 ◽  
Author(s):  
Guohong Zeng ◽  
Jin Li ◽  
Yuxiu Ma ◽  
Qian Pu ◽  
Tian Xiao ◽  
...  
Keyword(s):  
Root Rot ◽  
Molecular Mechanisms ◽  
Management Strategies ◽  
Panax Notoginseng ◽  
Glycoside Hydrolases ◽  
Rna Seq ◽  
Host Interaction ◽  
Excellent Starting Point ◽  
Starting Point ◽  
Genes Encoding

AbstractSaponins are kinds of antifungal compounds produced by Panax notoginseng to resist invasion by pathogens. Ilyonectria mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4H (Hours) and 12H (Hours) compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4H and 12H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation–reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen–Host Interaction) genes out of those 93 up-regulated genes. In this report, we analyzed virulence-associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

Evaluation of bio-agents and neem based products against late blight disease (Phytophthora infestans) of potato

2021 ◽  
Vol 74 (1) ◽  
pp. 181-187
Author(s):  
Mehi Lal ◽  
Sorabh Chaudhary ◽  
Sanjay Rawal ◽  
Sanjeev Sharma ◽  
Manoj Kumar ◽  
...  
Keyword(s):  
Late Blight ◽  
Phytophthora Infestans ◽  
Late Blight Disease ◽  
Blight Disease

scholarly journals Phenotypic Characterization of Recent Clonal Lineages of Phytophthora infestans in the United States

Plant Disease ◽  
2013 ◽  
Vol 97 (7) ◽  
pp. 873-881 ◽  
Author(s):  
G. Danies ◽  
I. M. Small ◽  
K. Myers ◽  
R. Childers ◽  
W. E. Fry
Keyword(s):  
United States ◽  
Late Blight ◽  
Phytophthora Infestans ◽  
The United States ◽  
Phenotypic Characterization ◽  
Phenotypic Traits ◽  
Mating Types ◽  
Late Blight Disease ◽  
Blight Disease

Phytophthora infestans, the causal agent of late blight disease, has been reported in the United States and Canada since the mid-nineteenth century. Due to the lack of or very limited sexual reproduction, the populations of P. infestans in the United States are primarily reproducing asexually and, thus, show a simple genetic structure. The emergence of new clonal lineages of P. infestans (US-22, US-23, and US-24) responsible for the late blight epidemics in the northeastern region of the United States in the summers of 2009 and 2010 stimulated an investigation into phenotypic traits associated with these genotypes. Mating type, differences in sensitivity to mefenoxam, differences in pathogenicity on potato and tomato, and differences in rate of germination were studied for clonal lineages US-8, US-22, US-23, and US-24. Both A1 and A2 mating types were detected. Lineages US-22, US-23, and US-24 were generally sensitive to mefenoxam while US-8 was resistant. US-8 and US-24 were primarily pathogenic on potato while US-22 and US-23 were pathogenic on both potato and tomato. Indirect germination was favored at lower temperatures (5 and 10°C) whereas direct germination, though uncommon, was favored at higher temperatures (20 and 25°C). Sporangia of US-24 released zoospores more rapidly than did sporangia of US-22 and US-23. The association of characteristic phenotypic traits with genotype enables the prediction of phenotypic traits from rapid genotypic analyses for improved disease management.

scholarly journals Global Histone H3 Lysine 4 Trimethylation (H3K4me3) Landscape Changes in Response to TGFβ

2021 ◽  
Vol 14 ◽  
pp. 251686572110517
Author(s):  
Ankit Naik ◽  
Nidhi Dalpatraj ◽  
Noopur Thakur
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Expression Patterns ◽  
Histone H3 ◽  
Epigenetic Mechanism ◽  
Stable Gene ◽  
Regulation Of Transcription ◽  
Functional Categories ◽  
Positive Regulation ◽  
Histone H4 Acetylation

TGFβ expression acts as a biomarker of poor prognosis in prostate cancer. It plays a dual functional role in prostate cancer. In the early stages of the tumor, it acts as a tumor suppressor while at the later stages of tumor development, it promotes metastasis. The molecular mechanisms of action of TGFβ are largely understood through the canonical and non-canonical signal transduction pathways. Our understanding of the mechanisms that establish transient TGFβ stimulation into stable gene expression patterns remains incomplete. Epigenetic marks like histone H3 modifications are directly linked with gene expression and they play an important role in tumorigenesis. In this report, we performed chromatin immunoprecipitation-sequencing (ChIP-Seq) to identify the genome-wide regions that undergo changes in histone H3 Lysine 4 trimethylation (H3K4me3) occupancy in response to TGFβ stimulation. We also show that TGFβ stimulation can induce acute epigenetic changes through the modulation of H3K4me3 signals at genes belonging to special functional categories in prostate cancer. TGFβ induces the H3K4me3 on its own ligands like TGFβ, GDF1, INHBB, GDF3, GDF6, BMP5 suggesting a positive feedback loop. The majority of genes were found to be involved in the positive regulation of transcription from the RNA polymerase II promoter in response to TGFβ. Other functional categories were intracellular protein transport, brain development, EMT, angiogenesis, antigen processing, antigen presentation via MHC class II, lipid transport, embryo development, histone H4 acetylation, positive regulation of cell cycle arrest, and genes involved in mitotic G2 DNA damage checkpoints. Our results link TGFβ stimulation to acute changes in gene expression through an epigenetic mechanism. These findings have broader implications on epigenetic bases of acute gene expression changes caused by growth factor stimulation.

Field application of Bacillus subtilis isolates for controlling late blight disease of potato caused by Phytophthora infestans

2019 ◽  
Vol 22 ◽  
pp. 101366 ◽  
Author(s):  
Bhimanagoud Kumbar ◽  
Riaz Mahmood ◽  
S.N. Nagesha ◽  
M.S. Nagaraja ◽  
D.G. Prashant ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Late Blight ◽  
Phytophthora Infestans ◽  
Field Application ◽  
Late Blight Disease ◽  
Blight Disease

scholarly journals Studies on Bd0934 and Bd3507, Two Secreted Nucleases from Bdellovibrio bacteriovorus, Reveal Sequential Release of Nucleases during the Predatory Cycle

2020 ◽  
Vol 202 (18) ◽  
Author(s):  
Ewa Bukowska-Faniband ◽  
Tilde Andersson ◽  
Rolf Lood
Keyword(s):  
Antibiotic Resistance ◽  
Life Cycle ◽  
Antibiotic Resistance Genes ◽  
Human Pathogens ◽  
Temporal Expression ◽  
Bdellovibrio Bacteriovorus ◽  
Exogenous Dna ◽  
Content Type ◽  
Genes Encoding ◽  
Predatory Bacteria

ABSTRACT Bdellovibrio bacteriovorus is an obligate predatory bacterium that invades and kills a broad range of Gram-negative prey cells, including human pathogens. Its potential therapeutic application has been the subject of increased research interest in recent years. However, an improved understanding of the fundamental molecular aspects of the predatory life cycle is crucial for developing this bacterium as a “living antibiotic.” During intracellular growth, B. bacteriovorus secretes an arsenal of hydrolases, which digest the content of the host cell to provide growth nutrients for the predator, e.g., prey DNA is completely degraded by the nucleases. Here, we have, on a genetic and molecular level, characterized two secreted DNases from B. bacteriovorus, Bd0934 and Bd3507, and determined the temporal expression profile of other putative secreted nucleases. We conclude that Bd0934 and Bd3507 are likely a part of the predatosome but are not essential for the predation, host-independent growth, prey biofilm degradation, and self-biofilm formation. The detailed temporal expression analysis of genes encoding secreted nucleases revealed that these enzymes are produced in a sequential orchestrated manner. This work contributes to our understanding of the sequential breakdown of the prey nucleic acid by the nucleases secreted during the predatory life cycle of B. bacteriovorus. IMPORTANCE Antibiotic resistance is a major global concern with few available new means to combat it. From a therapeutic perspective, predatory bacteria constitute an interesting tool. They not only eliminate the pathogen but also reduce the overall pool of antibiotic resistance genes through secretion of nucleases and complete degradation of exogenous DNA. Molecular knowledge of how these secreted DNases act will give us further insight into how antibiotic resistance, and the spread thereof, can be limited through the action of predatory bacteria.

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