scholarly journals Every cloud has a silver lining: how abiotic stresses affect gene expression in plant pathogen-interactions

2020 ◽  
Author(s):  
Marco Zarattini ◽  
Mahsa Farjad ◽  
Alban Launay ◽  
David Cannella ◽  
Marie-Christine Soulié ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Defense ◽  
Plant Pathogen ◽  
Abiotic Stresses ◽  
Biotic Interactions ◽  
Mineral Nutrient ◽  
Transcriptional Level ◽  
Tissue Organization ◽  
Plant Pathogen Interactions ◽  
The Impact

Abstract The current context of environmental and climate changes deeply influences the outcome of plant-pathogen interactions. Indeed, nowadays it is clear that abiotic stresses strongly affect biotic interactions at various levels. For instance, physiological parameters such as plant architecture and tissue organization along with primary and specialized metabolism are affected by environmental constraints, thus making the plant a more or less worthy host for a given pathogen. Moreover, abiotic stresses can affect the timely expression of plant defense and pathogen virulence. Indeed, several studies have shown that variations in temperature, water and mineral nutrient availability impact plant defense gene expression. Virulence gene expression, known to be crucial for disease outbreak, is also affected by environmental conditions, potentially modifying existing pathosystems and paving the way for emerging pathogens. The present review summarizes the current knowledge on the impact of abiotic stress on biotic interactions at the transcriptional level in both the plant and the pathogen side of the interaction. We performed a meta-data analysis of four different combinations of abiotic and biotic stresses. 197 modulated genes were common to all four combinations, with a strong defense-related GO term enrichment. We also describe the multistress-specific responses of selected defense-related genes.

scholarly journals Effector Biology in Focus: A Primer for Computational Prediction and Functional Characterization

2018 ◽  
Vol 31 (1) ◽  
pp. 22-33 ◽  
Author(s):  
Ronaldo J. D. Dalio ◽  
John Herlihy ◽  
Tiago S. Oliveira ◽  
John M. McDowell ◽  
Marcos Machado
Keyword(s):  
Disease Control ◽  
Plant Pathogen ◽  
Biological Diversity ◽  
Cell Structure ◽  
Functional Characterization ◽  
Computational Prediction ◽  
Effector Proteins ◽  
Immune Recognition ◽  
Plant Pathogen Interactions ◽  
The Impact

Plant–pathogen interactions are controlled by a multilayered immune system, which is activated by pathogen recognition in the host. Pathogens secrete effector molecules to interfere with the immune recognition or signaling network and reprogram cell structure or metabolism. Understanding the effector repertoires of diverse pathogens will contribute to unraveling the molecular mechanism of virulence and developing sustainable disease-control strategies for crops and natural ecosystems. Effector functionality has been investigated extensively in only a small number of pathogen species. However, many more pathogen genomes are becoming available, and much can be learned from a broader view of effector biology in diverse pathosystems. The purpose of this review is to summarize methodology for computational prediction of protein effectors, functional characterization of effector proteins and their targets, and the use of effectors as probes to screen for new sources of host resistance. Although these techniques were generally developed in model pathosystems, many of the approaches are directly applicable for exploration and exploitation of effector biology in pathosystems that are less well studied. We hope to facilitate such exploration, which will broaden understanding of the mechanisms that underpin the biological diversity of plant–pathogen interactions, and maximize the impact of new approaches that leverage effector biology for disease control.

scholarly journals Sperm and seminal plasma RNAs: what roles do they play beyond fertilization?

Reproduction ◽  
2019 ◽  
Vol 158 (4) ◽  
pp. R113-R123 ◽  
Author(s):  
Meritxell Jodar
Keyword(s):  
Gene Expression ◽  
Embryo Development ◽  
Seminal Plasma ◽  
Preimplantation Embryo ◽  
Epigenetic Inheritance ◽  
Early Embryo ◽  
Female Reproductive Tract ◽  
Transcriptional Level ◽  
Preimplantation Embryo Development ◽  
The Impact

The paternal contribution to the new individual is not just limited to half the diploid genome. Recent findings have shown that sperm delivers to the oocyte several components, including a complex population of RNAs, which may influence early embryo development and the long-term phenotype of the offspring. Although the majority of sperm RNAs may only represent spermatogenic leftovers with no further function, the male gamete provides a specific set of RNAs to the oocyte that is able to modulate gene expression in the preimplantation embryo. Those sperm transcripts include coding and non-coding RNAs that might either be translated by the oocyte machinery or directly regulate embryo gene expression at the transcriptional or post-transcriptional level. Interestingly, some sperm RNAs seem to be acquired during post-testicular maturation through active communication between sperm and epididymal and seminal exosomes released by the epididymis and the male accessory sex glands, respectively. Exosomes contained in the seminal plasma seem to not only interact with the spermatozoa but also with cells from the female reproductive tract, modulating their gene expression and influencing female immune response triggered by the semen. This review also considers the findings that indicate the role of semen RNAs in preimplantation embryo development and offspring phenotypes. In this regard, different studies supporting the hypothesis of paternal epigenetic inheritance of altered metabolic phenotypes associated with environmental exposures are discussed. Lastly, potential mechanisms that could explain the impact of semen RNAs to both early embryogenesis and paternal epigenetic inheritance are suggested.

Gene expression investigations on plant-pathogen interactions between Xanthomonas campestris pv. vesicatoria and pepper ( Capsicum annuum L.) using the cDNA-AFLP technology

2009 ◽  
Vol 57 (2) ◽  
pp. 127-136
Author(s):  
E. Szabó ◽  
G. Bárdos ◽  
I. Nagy
Keyword(s):  
Gene Expression ◽  
Capsicum Annuum ◽  
Plant Pathogen ◽  
Xanthomonas Campestris ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Bacterial Pathogen ◽  
Sequence Comparisons ◽  
Time Courses ◽  
Plant Pathogen Interactions

In order to target factors involved in plant-pathogen interactions, gene expression differences were investigated on pepper ( Capsicum annuum L.) plants after artificial infection with the bacterial pathogen Xanthomonas campestris pv. vesicatoria . Amplified Fragment Length Polymorphism investigations on reverse transcribed DNA fragments (cDNA-AFLP) were used to compare the expression profiles of parental lines and of resistant and susceptible individuals from pepper populations segregating for the gds gene, which confers a general defence system in pepper. In total, 73 transcript-derived fragments (TDFs) displaying differential expression patterns could be identified (presence-absence and/or different time courses in resistant and susceptible genotypes). Of these, 67 fragments were cloned and sequenced. In the case of several TDFs, sequence comparisons revealed close homologies to genes known to be responsible for abiotic stress or biotic elicitors, presenting potentially interesting targets for more detailed studies on gene expression and signal transduction.

Interspecies bacterial interactions stabilize transcriptional responses of ancestral wild types and biofilm-optimised variants

2020 ◽  
Author(s):  
Mette Burmølle ◽  
Nanna Mee Coops Olsen ◽  
Samuel Jacquiod ◽  
Henriette Lyng Røder
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Niche Partitioning ◽  
Gene Expression Profiles ◽  
Biotic Interactions ◽  
Culture Conditions ◽  
Differentially Expressed ◽  
Natural Environments ◽  
Transcriptional Responses ◽  
The Impact

<p>Most bacteria in natural environments live in multispecies biofilms, featuring high diversity and chemical heterogeneity. The cell-to-cell proximity found in these biofilms results in biotic interactions and niche-partitioning, facilitating co-existence of species that may otherwise out-compete each other. Additionally, due to the fast generation time of microbes and ceaseless biotic interactions, biofilms accelerate adaptation through the emergence of more fit genetic variants, most probably in response to niche-partitioning and local constraints. We have previously isolated and characterized biofilm-optimised (wrinkled) variants of <em>Xanthomonas retroflexus</em>. These variants emerged in biofilm co-cultures with <em>Paenibacillus amylolyticus</em> and reinforced the original interspecific mutualistic interaction, due to altered c-di-GMP regulation and spatial organisation.</p> <p>The aim of the present study was to examine the impact on gene expression profiles of either co-cultivation of the wild type (WT) or the wrinkled variant <em>X. retroflexus</em> with <em>P. amylolyticus</em> or its supernatant. We hypothesised that the gene expression of the two <em>X. retroflexus</em> strains would differ significantly and that these differences would be even more pronounced when co-cultured with <em>P. amylolyticus</em> or its supernatant.</p> <p>Mono- and dual species biofilms were grown in 24-well plates for 24 h. The liquid culture was removed, and the remaining biofilm from the sides of the wells and the air-liquid interface was sampled and processed for mRNA sequencing. After sequencing, <em>X. retroflexus </em>reads were mapped against its concatenated genome and genes of which expression differed by fold changes of log2 <-1 and >1 were considered differentially expressed.</p> <p>Unexpectedly, most marked differences in gene expression were observed when comparing mono-cultures of the WT and the wrinkled <em>X. retroflexus</em>, as approximately 500 genes were differentially expressed in these biofilms. Of these, 30 genes were predicted to encode biofilm-associated functions. When exposed to either live <em>P. amylolyticus</em> or its supernatant, expression profiles of the WT and the wrinkled variant were more similar, with the living partner <em>P. amylolyticus</em> being the key factor of this stabilization. Specifically, the stabilisation was caused by opposite regulation of specific genes in the wrinkled <em>X. retroflexus </em>variant compared to the WT in mono- vs. co-culture conditions.</p> <p>In conclusion, our data indicates that differences in gene expression of <em>X. retroflexus</em> WT and the biofilm-optimised variant were neutralised by co-cultivation with <em>P. amylolyticus</em>. To our knowledge, such comparative analyses of ancestral and biofilm-optimised variants have not previously been presented, despite being instrumental in elucidating evolutionary trajectories of such variants in complex environments.</p>

scholarly journals Compared to Australian Cultivars, European Summer Wheat (Triticum aestivum) Overreacts When Moderate Heat Stress Is Applied at the Pollen Development Stage

Agronomy ◽  
2018 ◽  
Vol 8 (7) ◽  
pp. 99 ◽  
Author(s):  
Kevin Begcy ◽  
Anna Weigert ◽  
Andrew Egesa ◽  
Thomas Dresselhaus
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Heat Waves ◽  
Negative Impact ◽  
Pollen Viability ◽  
Wheat Yield ◽  
Gene Expression Pattern ◽  
Type A ◽  
Transcriptional Level ◽  
The Impact

Heat stress frequently imposes a strong negative impact on vegetative and reproductive development of plants leading to severe yield losses. Wheat, a major temperate crop, is more prone to suffer from increased temperatures than most other major crops. With heat waves becoming more intense and frequent, as a consequence of global warming, a decrease in wheat yield is highly expected. Here, we examined the impact of a short-term (48 h) heat stress on wheat imposed during reproduction at the pollen mitosis stage both, at the physiological and molecular level. We analyzed two sets of summer wheat germplasms from Australia (Kukri, Drysdale, Gladius, and RAC875) and Europe (Epos, Cornetto, Granny, and Chamsin). Heat stress strongly affected gas exchange parameters leading to reduced photosynthetic and transpiration rates in the European cultivars. These effects were less pronounced in Australian cultivars. Pollen viability was also reduced in all European cultivars. At the transcriptional level, the largest group of heat shock factor genes (type A HSFs), which trigger molecular responses as a result of environmental stimuli, showed small variations in gene expression levels in Australian wheat cultivars. In contrast, HSFs in European cultivars, including Epos and Granny, were strongly downregulated and partly even silenced, while the high-yielding variety Chamsin displayed a strong upregulation of type A HSFs. In conclusion, Australian cultivars are well adapted to moderate heat stress compared to European summer wheat. The latter strongly react after heat stress application by downregulating photosynthesis and transpiration rates as well as differentially regulating HSFs gene expression pattern.

scholarly journals Plant genomics – celebrating plant health, plant biology and the impact of climate change on plant genomics

2020 ◽  
Vol 42 (4) ◽  
pp. 4-5
Keyword(s):  
Climate Change ◽  
Molecular Diagnostics ◽  
Plant Pathogen ◽  
Crop Protection ◽  
Plant Biology ◽  
Biosynthetic Pathways ◽  
Plant Genomics ◽  
New Applications ◽  
Plant Pathogen Interactions ◽  
The Impact

In this issue of The Biochemist, we explore plant genomics – from new applications for molecular diagnostics in crop protection and improving grain carbohydrates for human health to biosynthetic pathways and plant–pathogen interactions. We hope that you enjoy!

scholarly journals Brain histone beta-hydroxy-butyrylation couples metabolism with gene expression

2021 ◽  
Author(s):  
Sara Cornuti ◽  
Leonardo Lupori ◽  
Siwei Chen ◽  
Francesco Finamore ◽  
Muntaha Samad ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cerebral Cortex ◽  
Clock Genes ◽  
Neurological Diseases ◽  
Transcriptional Level ◽  
Functional Annotations ◽  
Ketogenic Diets ◽  
Brain Resilience ◽  
Beta Hydroxybutyrate ◽  
The Impact

The metabolic status has a well-documented influence on peripheral organs' physiology and pathology, however mounting evidence suggests that it can also affect brain function. For example, brain resilience to aging is enhanced by caloric restriction, and ketogenic diets have been used to treat neurological diseases. Unfortunately, little is known about the impact of metabolic stimuli on brain tissue at a molecular level. Recent data obtained in liver tissue suggest that beta-hydroxybutyrate (BHB) can also be a key signaling molecule regulating gene transcription. Thus, we adopted a ketogenic metabolic challenge, based on 48 hrs of fasting, and then assessed lysine beta-hydroxybutyrylation (K-bhb) levels in proteins extracted from the cerebral cortex. We found that fasting enhanced K-bhb in a variety of proteins and on histone H3. ChIP-seq experiments showed that K9 beta-hydroxybutyrylation of H3 (H3K9-bhb) was significantly enriched by fasting on more than 8000 DNA loci. Transcriptomic analysis showed that H3K9-bhb on enhancers and promoters correlated with active gene expression. Since one of the most enriched functional annotations both at the epigenetic and transcriptional level was circadian rhythms, we studied the expression of core-clock genes in the cortex during fasting. We found that the diurnal oscillation of specific transcripts was modulated at distinct times of the day along the circadian cycle. Thus, our results suggest that fasting dramatically impinges on the cerebral cortex transcriptional and epigenetic landscape, and BHB acts as a powerful epigenetic molecule in the brain through direct and specific histone marks remodelling in neural tissue cells.

scholarly journals RNA Interference: A Natural Immune System of Plants to Counteract Biotic Stressors

Cells ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 38 ◽  
Author(s):  
Tayeb Muhammad ◽  
Fei Zhang ◽  
Yan Zhang ◽  
Yan Liang
Keyword(s):  
Gene Expression ◽  
Immune System ◽  
Rna Interference ◽  
Transposable Elements ◽  
Plant Pathogen ◽  
Rna Silencing ◽  
Defense Mechanisms ◽  
Biological Process ◽  
Inhibit Gene Expression ◽  
Plant Pathogen Interactions

During plant-pathogen interactions, plants have to defend the living transposable elements from pathogens. In response to such elements, plants activate a variety of defense mechanisms to counteract the aggressiveness of biotic stressors. RNA interference (RNAi) is a key biological process in plants to inhibit gene expression both transcriptionally and post-transcriptionally, using three different groups of proteins to resist the virulence of pathogens. However, pathogens trigger an anti-silencing mechanism through the expression of suppressors to block host RNAi. The disruption of the silencing mechanism is a virulence strategy of pathogens to promote infection in the invaded hosts. In this review, we summarize the RNA silencing pathway, anti-silencing suppressors, and counter-defenses of plants to viral, fungal, and bacterial pathogens.

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