scholarly journals Biotrophic interactions disentangled: In situ localisation of mRNAs to decipher plant and algal pathogen – host interactions at the single cell level

2018 ◽  
Author(s):  
Julia Badstöber ◽  
Claire M. M. Gachon ◽  
Jutta Ludwig-Müller ◽  
Adolf M. Sandbichler ◽  
Sigrid Neuhauser
Keyword(s):  
Single Molecule ◽  
Plasmodiophora Brassicae ◽  
Plant Host ◽  
Host Interactions ◽  
Ectocarpus Siliculosus ◽  
Expression Of Genes ◽  
Algal Host ◽  
Microbe Interactions ◽  
Genome Model ◽  
Plant Pathogen Interactions

SummaryPlant-pathogen interactions follow spatiotemporal developmental dynamics where gene expression in pathogen and host undergo crucial changes. It is of great interest to detect, quantify and localise where and when key genes are active or inactive. Here, we adapt single molecule FISH techniques to demonstrate presence and activity of mRNAs using phytomyxids in their plant and algal host from laboratory and field materials. This allowed to monitor and quantify the expression of genes from the clubroot pathogen Plasmodiophora brassicae, several species of its Brassica hosts, and of several brown algae, including the genome model Ectocarpus siliculosus, infected with the phytomyxid Maullinia ectocarpii. We show that mRNAs are localised along a spatiotemporal gradient, thus providing proof-of-concept of the usefulness of these methods. These methods are easily adaptable to any interaction between microbes and their algal or plant host, and have the potential to increase our understanding of processes underpinning complex plant-microbe interactions.

scholarly journals Identification of lncRNAs Responsive to Infection by Plasmodiophora brassicae in Clubroot-Susceptible and -Resistant Brassica napus Lines Carrying Resistance Introgressed from Rutabaga

2019 ◽  
Vol 32 (10) ◽  
pp. 1360-1377 ◽  
Author(s):  
Aarohi Summanwar ◽  
Urmila Basu ◽  
Habibur Rahman ◽  
Nat Kav
Keyword(s):  
Brassica Napus ◽  
Target Genes ◽  
Plasmodiophora Brassicae ◽  
Genome Chromosome ◽  
Clubroot Disease ◽  
Brassica Crops ◽  
A Genome ◽  
Microbe Interactions ◽  
Trait Locus ◽  
Plant Pathogen Interactions

Clubroot disease, caused by Plasmodiophora brassicae Woronin, is a major threat to the production of Brassica’ crops. Resistance to different P. brassicae pathotypes has been reported in the A genome, chromosome A08; however, the molecular mechanism of this resistance, especially the involvement of long noncoding RNAs (lncRNAs), is not understood. We have used a strand-specific lncRNA-Seq approach to catalog lncRNAs from the roots of clubroot-susceptible and -resistant Brassica napus lines. In total, 530 differentially expressed (DE) lncRNAs were identified, including 88% of long intergenic RNAs and 11% natural antisense transcripts. Sixteen lncRNAs were identified as target mimics of the microRNAs (miRNAs) and eight were identified as the precursors of miRNAs. KEGG pathway analysis of the DE lncRNAs showed that the cis-regulated target genes mostly belong to the phenylpropanoid biosynthetic pathway (15%) and plant–pathogen interactions (15%) while the transregulated target genes mostly belong to carbon (18%) and amino acid biosynthesis pathway (19%). In all, 24 DE lncRNAs were identified from chromosome A08, which is known to harbor a quantitative trait locus conferring resistance to different P. brassicae pathotypes; however, eight of these lncRNAs showed expression only in the resistant plants. These results could form the basis for future studies aimed at delineating the roles of lncRNAs in plant–microbe interactions.

scholarly journals Organoids to Dissect Gastrointestinal Virus–Host Interactions: What Have We Learned?

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 999
Author(s):  
Sue E. Crawford ◽  
Sasirekha Ramani ◽  
Sarah E. Blutt ◽  
Mary K. Estes
Keyword(s):  
Cell Types ◽  
Human Infection ◽  
Viral Pathogens ◽  
Host Interactions ◽  
Complex Interactions ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Human Intestinal Epithelium ◽  
Human Viruses ◽  
Human Infections

Historically, knowledge of human host–enteric pathogen interactions has been elucidated from studies using cancer cells, animal models, clinical data, and occasionally, controlled human infection models. Although much has been learned from these studies, an understanding of the complex interactions between human viruses and the human intestinal epithelium was initially limited by the lack of nontransformed culture systems, which recapitulate the relevant heterogenous cell types that comprise the intestinal villus epithelium. New investigations using multicellular, physiologically active, organotypic cultures produced from intestinal stem cells isolated from biopsies or surgical specimens provide an exciting new avenue for understanding human specific pathogens and revealing previously unknown host–microbe interactions that affect replication and outcomes of human infections. Here, we summarize recent biologic discoveries using human intestinal organoids and human enteric viral pathogens.

scholarly journals Pseudomonas Lipopeptide-Mediated Biocontrol: Chemotaxonomy and Biological Activity

Molecules ◽  
2022 ◽  
Vol 27 (2) ◽  
pp. 372
Author(s):  
Feyisara Eyiwumi Oni ◽  
Qassim Esmaeel ◽  
Joseph Tobias Onyeka ◽  
Rasheed Adeleke ◽  
Cedric Jacquard ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
In Vitro Assays ◽  
Bacterial Physiology ◽  
Lineage Specificity ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
The One ◽  
Taxonomic Groups ◽  
Plant Pathogen Interactions

Pseudomonas lipopeptides (Ps-LPs) play crucial roles in bacterial physiology, host–microbe interactions and plant disease control. Beneficial LP producers have mainly been isolated from the rhizosphere, phyllosphere and from bulk soils. Despite their wide geographic distribution and host range, emerging evidence suggests that LP-producing pseudomonads and their corresponding molecules display tight specificity and follow a phylogenetic distribution. About a decade ago, biocontrol LPs were mainly reported from the P. fluorescens group, but this has drastically advanced due to increased LP diversity research. On the one hand, the presence of a close-knit relationship between Pseudomonas taxonomy and the molecule produced may provide a startup toolbox for the delineation of unknown LPs into existing (or novel) LP groups. Furthermore, a taxonomy–molecule match may facilitate decisions regarding antimicrobial activity profiling and subsequent agricultural relevance of such LPs. In this review, we highlight and discuss the production of beneficial Ps-LPs by strains situated within unique taxonomic groups and the lineage-specificity and coevolution of this relationship. We also chronicle the antimicrobial activity demonstrated by these biomolecules in limited plant systems compared with multiple in vitro assays. Our review further stresses the need to systematically elucidate the roles of diverse Ps-LP groups in direct plant–pathogen interactions and in the enhancement of plant innate immunity.

scholarly journals Transcription factor clusters regulate genes in eukaryotic cells

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Adam JM Wollman ◽  
Sviatlana Shashkova ◽  
Erik G Hedlund ◽  
Rosmarie Friemann ◽  
Stefan Hohmann ◽  
...  
Keyword(s):  
Single Molecule ◽  
Functional Unit ◽  
Yeast Genome ◽  
Gene Promoters ◽  
Intrinsically Disordered ◽  
Extracellular Signal ◽  
Genome Model ◽  
Nuclear Targets

Transcription is regulated through binding factors to gene promoters to activate or repress expression, however, the mechanisms by which factors find targets remain unclear. Using single-molecule fluorescence microscopy, we determined in vivo stoichiometry and spatiotemporal dynamics of a GFP tagged repressor, Mig1, from a paradigm signaling pathway of Saccharomyces cerevisiae. We find the repressor operates in clusters, which upon extracellular signal detection, translocate from the cytoplasm, bind to nuclear targets and turnover. Simulations of Mig1 configuration within a 3D yeast genome model combined with a promoter-specific, fluorescent translation reporter confirmed clusters are the functional unit of gene regulation. In vitro and structural analysis on reconstituted Mig1 suggests that clusters are stabilized by depletion forces between intrinsically disordered sequences. We observed similar clusters of a co-regulatory activator from a different pathway, supporting a generalized cluster model for transcription factors that reduces promoter search times through intersegment transfer while stabilizing gene expression.

scholarly journals Persistent virus integration into the genome of its algal host, Ectocarpus siliculosus (Phaeophyceae).

1999 ◽  
Vol 80 (6) ◽  
pp. 1367-1370 ◽  
Author(s):  
N Delaroque ◽  
I Maier ◽  
R Knippers ◽  
D G Müller
Keyword(s):  
Ectocarpus Siliculosus ◽  
Algal Host ◽  
Persistent Virus ◽  
Virus Integration

scholarly journals Acquisition of intact polar lipids from the prymnesiophyte <i>Phaeocystis globosa</i> by its lytic virus PgV-07T

2014 ◽  
Vol 11 (1) ◽  
pp. 185-194 ◽  
Author(s):  
D. S. Maat ◽  
N. J. Bale ◽  
E. C. Hopmans ◽  
A.-C. Baudoux ◽  
J. S. Sinninghe Damsté ◽  
...  
Keyword(s):  
Viral Infection ◽  
Lower Proportion ◽  
Specific Lipids ◽  
Phaeocystis Globosa ◽  
Host Interactions ◽  
Algal Virus ◽  
Host Interaction ◽  
Betaine Lipids ◽  
Algal Host ◽  
Intact Polar Lipids

Abstract. Recent studies showed changes in phytoplankton lipid composition during viral infection and have indicated roles for specific lipids in the mechanisms of algal virus-host interaction. To investigate the generality of these findings and obtain a better understanding of the allocation of specific lipids to viruses, we studied the intact polar lipid (IPL) composition of virally infected and non-infected cultures of the prymnesiophyte Phaeocystis globosa G(A) and its lytic virus PgV-07T. The P. globosa IPL composition was relatively stable over a diel cycle and not strongly affected by viral infection. Glycolipids, phospholipids and betaine lipids were present in both the host and virus, although specific groups such as the diacylglyceryl-hydroxymethyltrimethyl-β-alanines and the sulfoquinovosyldiacylglycerols, were present in a lower proportion or were not detected in the virus. Viral glycosphingolipids (vGSLs), which have been shown to play a role in the infection strategy of the virus EhV-86, infecting the prymnesiophyte Emiliania huxleyi CCMP374, were not encountered. Our results show that the involvement of lipids in virus–algal host interactions can be very different amongst virus–algal host systems.

scholarly journals Mucosal microbial parasites/symbionts in health and disease: an integrative overview

Parasitology ◽  
2019 ◽  
Vol 146 (9) ◽  
pp. 1109-1115 ◽  
Author(s):  
Robert P. Hirt
Keyword(s):  
Host Interactions ◽  
Detection Techniques ◽  
Symbiotic Relationships ◽  
Life Styles ◽  
Mucosal Surfaces ◽  
Microbe Interactions ◽  
Health And Disease ◽  
Host Microbe Interactions ◽  
Species Being

AbstractMicrobial parasites adapted to thrive at mammalian mucosal surfaces have evolved multiple times from phylogenetically distant lineages into various extracellular and intracellular life styles. Their symbiotic relationships can range from commensalism to parasitism and more recently some host–parasites interactions are thought to have evolved into mutualistic associations too. It is increasingly appreciated that this diversity of symbiotic outcomes is the product of a complex network of parasites–microbiota–host interactions. Refinement and broader use of DNA based detection techniques are providing increasing evidence of how common some mucosal microbial parasites are and their host range, with some species being able to swap hosts, including from farm and pet animals to humans. A selection of examples will illustrate the zoonotic potential for a number of microbial parasites and how some species can be either disruptive or beneficial nodes in the complex networks of host–microbe interactions disrupting or maintaining mucosal homoeostasis. It will be argued that mucosal microbial parasitic diversity will represent an important resource to help us dissect through comparative studies the role of host–microbe interactions in both human health and disease.

scholarly journals A circadian clock is essential for homeostasis of group 3 innate lymphoid cells in the gut

2019 ◽  
Vol 4 (40) ◽  
pp. eaax1215 ◽  
Author(s):  
Fei Teng ◽  
Jeremy Goc ◽  
Lei Zhou ◽  
Coco Chu ◽  
Manish A. Shah ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Target Genes ◽  
Innate Lymphoid Cells ◽  
Lymphoid Cells ◽  
Expression Of Genes ◽  
Microbe Interactions ◽  
Inflammatory Bowel ◽  
Group 3 ◽  
Host Microbe Interactions ◽  
Specific Deletion

Group 3 innate lymphoid cells (ILC3s) critically orchestrate host-microbe interactions in the healthy mammalian intestine and become substantially impaired in the context of inflammatory bowel disease (IBD). However, the molecular pathways controlling the homeostasis of ILC3s remain incompletely defined. Here, we identify that intestinal ILC3s are highly enriched in expression of genes involved in the circadian clock and exhibit diurnal oscillations of these pathways in response to light cues. Classical ILC3 effector functions also exhibited diurnal oscillations, and lineage-specific deletion of BMAL1, a master regulator of the circadian clock, resulted in markedly reduced ILC3s selectively in the intestine. BMAL1-deficient ILC3s exhibit impaired expression of Nr1d1 and Per3, hyperactivation of RORγt-dependent target genes, and elevated proapoptotic pathways. Depletion of the microbiota with antibiotics partially reduced the hyperactivation of BMAL1-deficient ILC3s and restored cellular homeostasis in the intestine. Last, ILC3s isolated from the inflamed intestine of patients with IBD exhibit substantial alterations in expression of several circadian-related genes. Our results collectively define that circadian regulation is essential for the homeostasis of ILC3s in the presence of a complex intestinal microbiota and that this pathway is disrupted in the context of IBD.

scholarly journals The ubiquitin system affects agronomic plant traits

2020 ◽  
Vol 295 (40) ◽  
pp. 13940-13955 ◽  
Author(s):  
Katrina J. Linden ◽  
Judy Callis
Keyword(s):  
Seed Size ◽  
Agronomic Traits ◽  
Plant Traits ◽  
Vascular Plant ◽  
Crop Improvement ◽  
26S Proteasome ◽  
Plant Host ◽  
Ubiquitin System ◽  
Expression Of Genes ◽  
Effector Recognition

In a single vascular plant species, the ubiquitin system consists of thousands of different proteins involved in attaching ubiquitin to substrates, recognizing or processing ubiquitinated proteins, or constituting or regulating the 26S proteasome. The ubiquitin system affects plant health, reproduction, and responses to the environment, processes that impact important agronomic traits. Here we summarize three agronomic traits influenced by ubiquitination: induction of flowering, seed size, and pathogen responses. Specifically, we review how the ubiquitin system affects expression of genes or abundance of proteins important for determining when a plant flowers (focusing on FLOWERING LOCUS C, FRIGIDA, and CONSTANS), highlight some recent studies on how seed size is affected by the ubiquitin system, and discuss how the ubiquitin system affects proteins involved in pathogen or effector recognition with details of recent studies on FLAGELLIN SENSING 2 and SUPPRESSOR OF NPR CONSTITUTIVE 1, respectively, as examples. Finally, we discuss the effects of pathogen-derived proteins on plant host ubiquitin system proteins. Further understanding of the molecular basis of the above processes could identify possible genes for modification or selection for crop improvement.

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