scholarly journals The RNAi Mechanism Regulates a New Exonuclease Gene Involved in the Virulence of Mucorales

2021 ◽  
Vol 22 (5) ◽  
pp. 2282
Author(s):  
Carlos Pérez-Arques ◽  
María Isabel Navarro-Mendoza ◽  
Laura Murcia ◽  
Eusebio Navarro ◽  
Victoriano Garre ◽  
...  
Keyword(s):  
Experimental Approach ◽  
Rnai Pathway ◽  
Biological Processes ◽  
Virulence Determinants ◽  
Proof Of Concept ◽  
Rnai Machinery ◽  
Opposite Behavior ◽  
New Treatments ◽  
Rnai Activity ◽  
Silence Gene

Mucormycosis is a lethal disease caused by Mucorales, which are emerging as human causes that explain the high mortality for this disease. Consequently, the research community is searching for virulence determinants that could be repurposed as targets to develop new treatments against mucormycosis. Our work explores an RNA interference (RNAi)-based approach to find targets involved in the virulence of Mucorales. A transcriptomewide analysis compared sRNAs and their target mRNAs in two Mucor lusitanicus different pathotypes, virulent and avirulent, generating a list of 75 loci selected by their differential sRNA accumulation in these strains. As a proof of concept and validity, an experimental approach characterized two loci showing opposite behavior, confirming that RNAi activity causes their differential expression in the two pathotypes. We generated deletion mutants for two loci and a knockin-strain overexpressing for one of these loci. Their functional analysis in murine virulence assays identified the gene wex1, a putative DEDDy exonuclease with RNase domains, as an essential factor for virulence. The identification of wex1 showed the potential of our approach to discover virulence factors not only in Mucorales but also in any other fungal model with an active RNAi machinery. More importantly, it adds a new layer to the biological processes controlled by RNAi in M. lusitanicus, confirming that the Dicer-dependent RNAi pathway can silence gene expression to promote virulence.

scholarly journals The RNAi Mechanism Regulates a New Exonuclease Gene Involved in the Virulence of Mucorales

2021 ◽  
Author(s):  
Carlos Pérez Arques ◽  
María Isabel Navarro-Mendozo ◽  
Laura Murcia ◽  
Eusebio Navarro ◽  
Victoriano Garre ◽  
...  
Keyword(s):  
Experimental Approach ◽  
Rnai Pathway ◽  
Virulence Determinants ◽  
Proof Of Concept ◽  
Human Pathogens ◽  
Rnai Machinery ◽  
Opposite Behavior ◽  
New Treatments ◽  
Rnai Activity ◽  
Silence Gene

Mucormycosis is a lethal disease caused by Mucorales, which are emerging as human pathogens with virulent behavior. Antifungal resistance and ineffective treatments are two major causes that explain the high mortality for this disease. Consequently, the research community is searching for virulence determinants that could be repurposed as targets to develop new treatments against mucormycosis. Our work explores an RNA interference (RNAi)-based approach to find targets involved in the virulence of Mucorales. A transcriptome-wide analysis compared sRNAs and their target mRNAs in two Mucor lusitanicus different pathotypes, virulent and avirulent, generating a list of 75 loci selected by their differential sRNA accumulation in these strains. As a proof of concept and validity, an experimental approach characterized two loci showing opposite behavior, confirming that RNAi activity causes their differential expression in the two pathotypes. We generated deletion mutants for two loci and a knockin-strain overexpressing for one these loci. Their functional analysis in murine virulence assays identified the gene wex1, a putative DEDDy exonuclease with RNase domains, as an essential factor for virulence. The identification of wex1 showed the potential of our approach to discover virulence factors not only in Mucorales but also in any other fungal model with an active RNAi machinery. But, more importantly, it adds a new layer to the biological processes controlled by RNAi in M. lusitanicus, confirming that the Dicer-dependent RNAi pathway can silence gene expression to promote virulence.

scholarly journals Environmental RNA interference in two-spotted spider mite, Tetranychus urticae, reveals dsRNA processing requirements for efficient RNAi response

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Nicolas Bensoussan ◽  
Sameer Dixit ◽  
Midori Tabara ◽  
David Letwin ◽  
Maja Milojevic ◽  
...  
Keyword(s):  
Rna Interference ◽  
Tetranychus Urticae ◽  
Pest Control ◽  
Spider Mite ◽  
26S Proteasome ◽  
Rnai Pathway ◽  
Rnai Machinery ◽  
Two Spotted Spider Mite ◽  
Species Specific

Abstract Comprehensive understanding of pleiotropic roles of RNAi machinery highlighted the conserved chromosomal functions of RNA interference. The consequences of the evolutionary variation in the core RNAi pathway genes are mostly unknown, but may lead to the species-specific functions associated with gene silencing. The two-spotted spider mite, Tetranychus urticae, is a major polyphagous chelicerate pest capable of feeding on over 1100 plant species and developing resistance to pesticides used for its control. A well annotated genome, susceptibility to RNAi and economic importance, make T. urticae an excellent candidate for development of an RNAi protocol that enables high-throughput genetic screens and RNAi-based pest control. Here, we show that the length of the exogenous dsRNA critically determines its processivity and ability to induce RNAi in vivo. A combination of the long dsRNAs and the use of dye to trace the ingestion of dsRNA enabled the identification of genes involved in membrane transport and 26S proteasome degradation as sensitive RNAi targets. Our data demonstrate that environmental RNAi can be an efficient reverse genetics and pest control tool in T. urticae. In addition, the species-specific properties together with the variation in the components of the RNAi machinery make T. urticae a potent experimental system to study the evolution of RNAi pathways.

scholarly journals Environmental RNA interference in two-spotted spider mite, Tetranychus urticae, reveals dsRNA processing requirements for efficient RNAi response

2020 ◽  
Author(s):  
Nicolas Bensoussan ◽  
Sameer Dixit ◽  
Midori Tabara ◽  
David Letwin ◽  
Maja Milojevic ◽  
...  
Keyword(s):  
Rna Interference ◽  
Tetranychus Urticae ◽  
Pest Control ◽  
Spider Mite ◽  
26S Proteasome ◽  
Rnai Pathway ◽  
Rnai Machinery ◽  
Two Spotted Spider Mite ◽  
Species Specific

AbstractComprehensive understanding of pleiotropic roles of RNAi machinery highlighted the conserved chromosomal functions of RNA interference. The consequences of the evolutionary variation in the core RNAi pathway genes are mostly unknown, but may lead to the species-specific functions associated with gene silencing. The two-spotted spider mite, Tetranychus urticae, is a major polyphagous chelicerate pest capable of feeding on over 1,100 plant species and developing resistance to pesticides used for its control. A well annotated genome, susceptibility to RNAi and economic importance, make T. urticae an excellent candidate for development of an RNAi protocol that enables high-throughput genetic screens and RNAi-based pest control. Here, we show that the length of the exogenous dsRNA critically determines its processivity and ability to induce RNAi in vivo. A combination of the long dsRNAs and the use of dye to trace the ingestion of dsRNA enabled the identification of genes involved in membrane transport and 26S proteasome degradation as sensitive RNAi targets. Our data demonstrate that environmental RNAi can be an efficient reverse genetics and pest control tool in T. urticae. In addition, the species-specific properties together with the variation in the components of the RNAi machinery make T. urticae a potent experimental system to study the evolution of RNAi pathways.

scholarly journals Role of the Non-Canonical RNAi Pathway in the Antifungal Resistance and Virulence of Mucorales

2021 ◽  
Author(s):  
José Tomás Cánovas-Márquez ◽  
María Isabel Navarro-Mendoza ◽  
Carlos Pérez-Arques ◽  
Carlos Lax ◽  
Ghizlane Tahiri ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Genome Stability ◽  
Antifungal Drug ◽  
Rnai Pathway ◽  
Ribonuclease Iii ◽  
Functional Roles ◽  
Antifungal Drug Resistance ◽  
Promising Target ◽  
New Treatments ◽  
Drug Resistant Strains

Mucorales are the causal agents for the lethal disease known as mucormycosis. Mortality rates of mucormycosis can reach up to 90%, due to the mucoralean antifungal drug resistance and the lack of effective therapies. A concerning urgency among the medical and scientific community claims to find targets for the development of new treatments. Here, we reviewed different studies de-scribing the role and machinery of a novel non-canonical RNAi pathway (NCRIP) only conserved in Mucorales. Its non-canonical features are the independence of Dicer and Argonautes proteins. Conversely, NCRIP relies on RNA-dependent RNA Polymerases and an atypical ribonuclease III (RNaseIII). NCRIP regulates the expression of mRNAs by degrading them in a specific manner. Its mechanism binds dsRNA but only cuts ssRNA. NCRIP exhibits a diversity of functional roles. It represses the epimutational pathway and the lack of NCRIP increases the generation of drug resistant strains. NCRIP also regulates the control of retrotransposons expression, playing an essential role in genome stability. Finally, NCRIP regulates the response during phagocytosis, affecting the multifactorial process of virulence. These critical NCRIP roles in virulence and antifungal drug resistance, along with its exclusive presence in Mucorales, mark this pathway as a promising target to fight against mucormycosis.

scholarly journals Self-restoration of cardiac excitation rhythm by anti-arrhythmic ion channel gating

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Rupamanjari Majumder ◽  
Tim De Coster ◽  
Nina Kudryashova ◽  
Arie O Verkerk ◽  
Ivan V Kazbanov ◽  
...  
Keyword(s):  
Ventricular Arrhythmias ◽  
Experimental Validation ◽  
Cardiac Tissue ◽  
Ionic Current ◽  
Dynamic Clamp ◽  
Biological Processes ◽  
Proof Of Concept ◽  
Atrial Myocytes ◽  
Channel Current ◽  
Cardiac Excitation

Homeostatic regulation protects organisms against hazardous physiological changes. However, such regulation is limited in certain organs and associated biological processes. For example, the heart fails to self-restore its normal electrical activity once disturbed, as with sustained arrhythmias. Here we present proof-of-concept of a biological self-restoring system that allows automatic detection and correction of such abnormal excitation rhythms. For the heart, its realization involves the integration of ion channels with newly designed gating properties into cardiomyocytes. This allows cardiac tissue to i) discriminate between normal rhythm and arrhythmia based on frequency-dependent gating and ii) generate an ionic current for termination of the detected arrhythmia. We show in silico, that for both human atrial and ventricular arrhythmias, activation of these channels leads to rapid and repeated restoration of normal excitation rhythm. Experimental validation is provided by injecting the designed channel current for arrhythmia termination in human atrial myocytes using dynamic clamp.

scholarly journals Expression Dynamics of Core RNAi Machinery Genes in Pea Aphids Upon Exposure to Artificially Synthesized dsRNA and miRNAs

Insects ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 70 ◽  
Author(s):  
Li Yang ◽  
Yuan Tian ◽  
Yuan-Yuan Peng ◽  
Jinzhi Niu ◽  
Jin-Jun Wang
Keyword(s):  
Rnai Pathway ◽  
Dependent Manner ◽  
Rnai Machinery ◽  
Related Factors ◽  
Pea Aphids ◽  
Important Pest ◽  
Mirna Pathway ◽  
Pirna Pathway ◽  
Sirna Pathway ◽  
Core Genes

The pea aphid is an important pest of vegetables and causes serious losses worldwide. RNA interference (RNAi) is an effective pest control tool, and three sub-pathways have been described: The miRNA pathway, siRNA pathway, and piRNA pathway. A large number of genes in miRNA pathway and piRNA pathway are found to be expanded. To study the roles of these genes, the expression of 25 core RNAi genes was screened in spatiotemporal samples, artificially synthesized dsRNA and miRNA treated samples. The 25 genes were all expressed during different development stages and in different tissues. In dsRNA-treated samples and miRNA-treated samples, the expressions of genes in these three pathways were induced, especially the expanded genes. This suggests a complex network of RNAi core genes in the three sub-pathways. Treatment of miRNA seems to induce gene expression in a dosage-dependent manner. These results increase our knowledge of the siRNA pathway and related factors from RNAi pathway in aphids and promote the use of RNAi for the control of aphid pests.

scholarly journals Ago1 Affects the Virulence of the Fungal Plant Pathogen Zymoseptoria tritici

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1011
Author(s):  
Michael Habig ◽  
Klaas Schotanus ◽  
Kim Hufnagel ◽  
Petra Happel ◽  
Eva H. Stukenbrock
Keyword(s):  
Plant Pathogen ◽  
Allelic Diversity ◽  
Rnai Pathway ◽  
Chromosome Stability ◽  
In Planta ◽  
Zymoseptoria Tritici ◽  
Rnai Machinery ◽  
Fungal Plant Pathogen ◽  
Host Infection

In host-pathogen interactions RNA interference (RNAi) has emerged as a pivotal mechanism to modify both, the immune responses of the host as well as the pathogenicity and virulence of the pathogen. In addition, in some fungi RNAi is also known to affect chromosome biology via its effect on chromatin conformation. Previous studies reported no effect of the RNAi machinery on the virulence of the fungal plant pathogen Zymoseptoria tritici however the role of RNAi is still poorly understood in this species. Herein, we elucidate whether the RNAi machinery is conserved within the genus Zymoseptoria. Moreover, we conduct functional analyses of Argonaute and Dicer-like proteins and test if the RNAi machinery affects chromosome stability. We show that the RNAi machinery is conserved among closely related Zymoseptoria species while an exceptional pattern of allelic diversity was possibly caused by introgression. The deletion of Ago1 reduced the ability of the fungus to produce asexual propagules in planta in a quantitative matter. Chromosome stability of the accessory chromosome of Z. tritici was not prominently affected by the RNAi machinery. These results indicate, in contrast to previous finding, a role of the RNAi pathway during host infection, but not in the stability of accessory chromosomes in Z. tritici.

scholarly journals Autoencoder and Optimal Transport to Infer Single-Cell Trajectories of Biological Processes

2018 ◽  
Author(s):  
Karren Dai Yang ◽  
Karthik Damodaran ◽  
Saradha Venkatchalapathy ◽  
Ali C. Soylemezoglu ◽  
G.V. Shivashankar ◽  
...  
Keyword(s):  
Single Cell ◽  
Optimal Transport ◽  
Chromatin Condensation ◽  
Breast Cancer Cell Lines ◽  
Biological Processes ◽  
Proof Of Concept ◽  
Tissue Samples ◽  
Early Biomarkers ◽  
Latent Space ◽  
Cell Trajectories

AbstractAlthough we can increasingly image and measure biological processes at single-cell resolution, most assays can only take snapshots from a population of cells in time. Here we describe ImageAEOT, which combines an AutoEncoder, to map single-cell Images from different cell populations to a common latent space, with the framework of Optimal Transport to infer cellular trajectories. As a proof-of-concept, we apply ImageAEOT to nuclear and chromatin images during the activation of fibroblasts by tumor cells in engineered 3D tissues. We further validate ImageAEOT on chromatin images of various breast cancer cell lines and human tissue samples, thereby linking alterations in chromatin condensation patterns to different stages of tumor progression. Importantly, ImageAEOT can infer the trajectory of a particular cell from one snapshot in time and identify the changing features to provide early biomarkers for developmental and disease progression.

scholarly journals Detection of methylation, acetylation and glycosylation of protein residues by monitoring 13C chemical-shift changes

2016 ◽  
Author(s):  
Pablo G. Garay ◽  
Osvaldo A. Martin ◽  
Harold A. Scheraga ◽  
Jorge A. Vila
Keyword(s):  
Chemical Shift ◽  
Chemical Shifts ◽  
Biological Processes ◽  
Proof Of Concept ◽  
Post Translational Modifications ◽  
13C Chemical Shifts ◽  
Protein Residues ◽  
Lysine Residues ◽  
13C Chemical Shift ◽  
Good Agreement

Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here, as a proof-of-concept, the feasibility of using 13C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the 13C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a validation test of this approach, we compare our theoretical computations of the 13Ce chemical-shift values against experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ~1 ppm. Then, further use of this approach to select the most suitable 13C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results.

Sign in / Sign up

Export Citation Format

Share Document