A genome-wide screening for RNAi pathway proteins in Acari

Abstract Background RNA interference (RNAi) is a highly conserved, sequence-specific gene silencing mechanism present in Eukaryotes. Three RNAi pathways are known, namely micro-RNA (miRNA), piwi-interacting RNA (piRNA) and short interfering RNA (siRNA). However, little knowledge exists about the proteins involved in these pathways in Acari. Moreover, variable successes has been obtained in gene knockdown via siRNA pathway in their functional genomics and management. We hypothesized that the clue may be in the variability of the composition and the efficacy of siRNA machinery among Acari. Results Both comparative genomic analyses and domain annotation suggest that all the analyzed species have homologs of putative core proteins that mediate cleaving of targeted genes via the three RNAi pathways. We identified putative homologs of Caenorhabditis elegans RNA-dependent RNA polymerase (RdRP) protein in all species though no secondary Argonaute homologs that operate with this protein in siRNA amplification mechanism were found, suggesting that the siRNA amplification mechanism present in Acari may be distinct from that described in C. elegans. Moreover, the genomes of these species do not encode homologs of C. elegans systemic RNAi defective-1 (Sid-1) protein that mediate silencing of the mRNA target throughout the treated organisms suggesting that the phenomena of systemic RNAi that has been reported in some Acari species probably occur through a different mechanism. However, homologs of putative RNAi spreading defective-3 (Rsd-3) protein and scavenger receptors namely Eater and SR-CI that mediate endocytosis cellular update of dsRNA in C. elegans and Drosophila melanogaster were found in Acari genomes. This result suggests that cellular dsRNA uptake in Acari is endocytosis-dependent. Detailed phylogenetic analyses of core RNAi pathway proteins in the studied species revealed that their evolution is compatible with the proposed monophyletic evolution of this group. Conclusions Our analyses have revealed the potential activity of all three pathways in Acari. Still, much experimental work remains to be done to confirm the mechanisms behind these pathways in particular those that govern systemic/parental RNAi and siRNA amplification in Acari. Disclosure of these mechanisms will facilitate the development of new and specific management tools for the harmful species and enrichment of the beneficial species.

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A genome-wide screening for RNAi pathway proteins in Acari

10.21203/rs.3.rs-38229/v4 ◽

2020 ◽

Author(s):

Beatrice T Nganso ◽

Noa Sela ◽

Victoria Soroker

Keyword(s):

Micro Rna ◽

Rnai Pathway ◽

Comparative Genomic ◽

Specific Gene ◽

C Elegans ◽

Conserved Sequence ◽

Core Proteins ◽

A Genome ◽

Systemic Rnai ◽

Amplification Mechanism

Abstract Background: RNA interference (RNAi) is a highly conserved, sequence-specific gene silencing mechanism present in Eukaryotes. Three RNAi pathways are known, namely micro-RNA (miRNA), piwi-interacting RNA (piRNA) and short interfering RNA (siRNA). However, little knowledge exists about the proteins involved in these pathways in Acari. Moreover, variable successes has been obtained in gene knockdown via siRNA pathway in their functional genomics and management. We hypothesized that the clue may be in the variability of the composition and the efficacy of siRNA machinery among Acari.Results: Both comparative genomic analyses and domain annotation suggest that all the analyzed species have homologs of putative core proteins that mediate cleaving of targeted genes via the three RNAi pathways. We identified putative homologs of Caenorhabditis elegans RNA-dependent RNA polymerase (RdRP) protein in all species though no secondary Argonaute homologs that operate with this protein in siRNA amplification mechanism were found, suggesting that the siRNA amplification mechanism present in Acari may be distinct from that described in C. elegans. Moreover, the genomes of these species do not encode homologs of C. elegans systemic RNAi defective-1 (Sid-1) protein that mediate silencing of the mRNA target throughout the treated organisms suggesting that the phenomena of systemic RNAi that has been reported in some Acari species probably occur through a different mechanism. However, homologs of putative RNAi spreading defective-3 (Rsd-3) protein and scavenger receptors namely Eater and SR-CI that mediate endocytosis cellular update of dsRNA in C. elegans and Drosophila melanogaster were found in Acari genomes. This result suggests that cellular dsRNA uptake in Acari is endocytosis-dependent. Detailed phylogenetic analyses of core RNAi pathway proteins in the studied species revealed that their evolution is compatible with the proposed monophyletic evolution of this group.Conclusions: Our analyses have revealed the potential activity of all three pathways in Acari. Still, much experimental work remains to be done to confirm the mechanisms behind these pathways in particular those that govern systemic/parental RNAi and siRNA amplification in Acari. Disclosure of these mechanisms will facilitate the development of new and specific management tools for the harmful species and enrichment of the beneficial species.

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A genome-wide screening for RNAi pathway proteins in Acari

10.21203/rs.3.rs-38229/v3 ◽

2020 ◽

Author(s):

Beatrice T Nganso ◽

Noa Sela ◽

Victoria Soroker

Keyword(s):

Micro Rna ◽

Rnai Pathway ◽

Comparative Genomic ◽

Specific Gene ◽

C Elegans ◽

Conserved Sequence ◽

Core Proteins ◽

A Genome ◽

Systemic Rnai ◽

Amplification Mechanism

Abstract BackgroundRNA interference (RNAi) is a highly conserved, sequence-specific gene silencing mechanism present in Eukaryotes. Three RNAi pathways are known, namely micro-RNA (miRNA), Piwi-interacting RNA (piRNA) and short interfering RNA (siRNA). However, little knowledge exists about the proteins involved in these pathways in Acari. Moreover, variable successes has been obtained in gene knockdown via siRNA pathway in their functional genomics and management. We hypothesized that the clue may be in the variability of the composition and the efficacy of siRNA machinery among Acari.ResultsBoth comparative genomic analyses and domain annotation suggest that all the analyzed species have homologs of putative core proteins that mediate cleaving of targeted genes via the three RNAi pathways. We identified putative homologs of Caenorhabditis elegans RNA-dependent RNA polymerase (RdRP) protein in all species though no secondary Argonaute homologs that operate with this protein in siRNA amplification mechanism were found, suggesting that the siRNA amplification mechanism present in Acari may be distinct from that described in C. elegans. Moreover, the genomes of these species do not encode homologs of C. elegans systemic RNAi defective 1 (Sid-1) protein that mediate silencing of the mRNA target throughout the treated organisms suggesting that the phenomena of systemic RNAi that has been reported in some Acari species probably occur through a different mechanism. However, Homologs of putative RNAi spreading defective-3 (Rsd-3) protein and scavenger receptors namely Eater and SR-CI that mediate endocytosis cellular update of dsRNA in C. elegans and Drosophila melanogaster were found in Acari genomes. This result suggests that cellular dsRNA uptake in Acari is endocytosis-dependent. Detailed phylogenetic analyses of core RNAi pathway proteins in the studied species revealed that their evolution is compatible with the proposed monophyletic evolution of this group.ConclusionsOur analyses have revealed the potential activity of all three pathways in Acari. Still, much experimental work remains to be done to confirm the mechanisms behind these pathways in particular those that govern systemic/parental RNAi and siRNA amplification in Acari. Disclosure of these mechanisms will facilitate the development of new and specific management tools for the harmful species and enrichment of the beneficial species.

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A genome-wide screening for RNAi pathway proteins in Acari

10.21203/rs.3.rs-38229/v2 ◽

2020 ◽

Author(s):

Beatrice T Nganso ◽

Noa Sela ◽

Victoria Soroker

Keyword(s):

Gene Silencing ◽

Micro Rna ◽

Rnai Pathway ◽

Comparative Genomic ◽

Specific Gene ◽

C Elegans ◽

Conserved Sequence ◽

A Genome ◽

Systemic Rnai ◽

Amplification Mechanism

Abstract Background RNA interference (RNAi) is a highly conserved, sequence-specific gene silencing mechanism present in Eukaryotes. Three RNAi pathways critical for organismal development and survival are known, namely micro-RNA (miRNA), Piwi-interacting RNA (piRNA) and short interfering RNA (siRNA) pathways. Little knowledge exist about the genes involved in these pathways in Acari. Moreover, variable successes has been obtained in gene knockdown via siRNA pathway in functional genomics and management of Acari species. We hypothesized that the clue may be in the variability in the composition and the efficacy of siRNAi machinery among Acari. Results Both comparative genomic analyses and domain annotation suggest that all the analyzed species have orthologs of genes that mediate gene silencing via the three RNAi pathways though gene duplication and/or loss have occurred in the different species. We also identified orthologs of Caenorhabditis elegans RNA-dependent RNA polymerase (RdRP) gene in all Acari species though no secondary Argonaute homologs that operate with this gene in siRNA amplification mechanism were found. This finding suggests that the siRNA amplification mechanism present in Acari may be distinct from that described in C. elegans . Moreover, the genomes of these Acari species encode no ortholog of C. elegans systemic RNAi defective 1 (Sid-1) that mediate systemic RNAi, suggesting that the phenomena of systemic and parental RNAi that has been reported in some Acari species probably occur through a different mechanism. Orthologs of RNAi spreading defective-3 (Rsd-3) gene and scavenger receptors namely Eater and SR-CI that mediate endocytosis cellular update of dsRNA in C. elegans and Drosophila melanogaster were found in Acari genomes. This result suggests that cellular dsRNA uptake in Acari is endocytosis-dependent. Detailed phylogenetic analyses of core RNAi pathway genes in the studied Acari species revealed that their evolution is compatible with the proposed monophyletic evolution of this group. Conclusions Taken together, our in silico comparative analyses have revealed the potential activity of all three pathways in Acari. However, much experimental work remains to be done in elucidating the operating mechanisms behind these pathways in particular those that govern systemic/parental RNAi and siRNA amplification in Acari.

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A genome-wide screening for RNAi pathway genes in Acari

10.21203/rs.3.rs-38229/v1 ◽

2020 ◽

Author(s):

Victoria Soroker ◽

Beatrice T Nganso ◽

Noa Sela

Keyword(s):

Gene Silencing ◽

Micro Rna ◽

Rnai Pathway ◽

Comparative Genomic ◽

Specific Gene ◽

C Elegans ◽

Conserved Sequence ◽

A Genome ◽

Systemic Rnai ◽

Amplification Mechanism

Abstract BackgroundRNA interference (RNAi) is a highly conserved, sequence-specific gene silencing mechanism present in Eukaryotes. Three RNAi pathways critical for organismal development and survival are known, namely micro-RNA (miRNA), Piwi-interacting RNA (piRNA) and short interfering RNA (siRNA) pathways. Little knowledge exist about the genes involved in these pathways in Acari. Moreover, variable successes has been obtained in gene knockdown via siRNA pathway in functional genomics and management of Acari species. We hypothesized that the clue may be in the variability in the composition and the efficacy of siRNAi machinery among Acari. ResultsBoth comparative genomic analyses and domain annotation suggest that all the analyzed species have orthologs of genes that mediate gene silencing via the three RNAi pathways though gene duplication and/or loss have occurred in the different species. We also identified orthologs of Caenorhabditis elegans RNA-dependent RNA polymerase (RdRP) gene in all Acari species though no secondary Argonaute homologs that operate with this gene in siRNA amplification mechanism were found. This finding suggests that the siRNA amplification mechanism present in Acari may be distinct from that described in C. elegans. Moreover, the genomes of these Acari species encode no ortholog of C. elegans systemic RNAi defective 1 (Sid-1) that mediate systemic RNAi, suggesting that the phenomena of systemic and parental RNAi that has been reported in some Acari species probably occur through a different mechanism. Orthologs of RNAi spreading defective-3 (Rsd-3) gene and scavenger receptors namely Eater and SR-CI that mediate endocytosis cellular update of dsRNA in C. elegans and Drosophila melanogaster were found in Acari genomes. This result suggests that cellular dsRNA uptake in Acari is endocytosis-dependent. Detailed phylogenetic analyses of core RNAi pathway genes in the studied Acari species revealed that their evolution is compatible with the proposed monophyletic evolution of this group.ConclusionsTaken together, our in silico comparative analyses have revealed the potential activity of all three pathways in Acari. However, much experimental work remains to be done in elucidating the operating mechanisms behind these pathways in particular those that govern systemic/parental RNAi and siRNA amplification in Acari.

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A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity

eLife ◽

10.7554/elife.00994 ◽

2013 ◽

Vol 2 ◽

Cited By ~ 91

Author(s):

Alyson Ashe ◽

Tony Bélicard ◽

Jérémie Le Pen ◽

Peter Sarkies ◽

Lise Frézal ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Genome Wide Association Study ◽

Rna Virus ◽

Rnai Pathway ◽

Animal Cells ◽

C Elegans ◽

Base Pair Deletion ◽

A Genome ◽

Positive Strand Rna ◽

Viral Recognition

RNA interference defends against viral infection in plant and animal cells. The nematode Caenorhabditis elegans and its natural pathogen, the positive-strand RNA virus Orsay, have recently emerged as a new animal model of host-virus interaction. Using a genome-wide association study in C. elegans wild populations and quantitative trait locus mapping, we identify a 159 base-pair deletion in the conserved drh-1 gene (encoding a RIG-I-like helicase) as a major determinant of viral sensitivity. We show that DRH-1 is required for the initiation of an antiviral RNAi pathway and the generation of virus-derived siRNAs (viRNAs). In mammals, RIG-I-domain containing proteins trigger an interferon-based innate immunity pathway in response to RNA virus infection. Our work in C. elegans demonstrates that the RIG-I domain has an ancient role in viral recognition. We propose that RIG-I acts as modular viral recognition factor that couples viral recognition to different effector pathways including RNAi and interferon responses.

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Pseudomonas donghuensis HYS gtrA/B/II Gene Cluster Contributes to Its Pathogenicity toward Caenorhabditis elegans

International Journal of Molecular Sciences ◽

10.3390/ijms221910741 ◽

2021 ◽

Vol 22 (19) ◽

pp. 10741

Author(s):

Yaqian Xiao ◽

Panning Wang ◽

Xuesi Zhu ◽

Zhixiong Xie

Keyword(s):

Caenorhabditis Elegans ◽

Gene Cluster ◽

Mapk Pathway ◽

Genomic Analysis ◽

Virulence Gene ◽

Comparative Genomic ◽

Specific Gene ◽

C Elegans ◽

O Antigen ◽

Specific Virulence

Pseudomonas donghuensis HYS is more virulent than P. aeruginosa toward Caenorhabditis elegans but the mechanism underlying virulence is unclear. This study is the first to report that the specific gene cluster gtrA/B/II in P. donghuensis HYS is involved in the virulence of this strain toward C. elegans, and there are no reports of GtrA, GtrB and GtrII in any Pseudomonas species. The pathogenicity of P. donghuensis HYS was evaluated using C. elegans as a host. Based on the prediction of virulence factors and comparative genomic analysis of P. donghuensis HYS, we identified 42 specific virulence genes in P. donghuensis HYS. Slow-killing assays of these genes showed that the gtrAB mutation had the greatest effect on the virulence of P. donghuensis HYS, and GtrA, GtrB and GtrII all positively affected P. donghuensis HYS virulence. Two critical GtrII residues (Glu47 and Lys480) were identified in P. donghuensis HYS. Transmission electron microscopy (TEM) showed that GtrA, GtrB and GtrII were involved in the glucosylation of lipopolysaccharide (LPS) O-antigen in P. donghuensis HYS. Furthermore, colony-forming unit (CFU) assays showed that GtrA, GtrB and GtrII significantly enhanced P. donghuensis HYS colonization in the gut of C. elegans, and glucosylation of LPS O-antigen and colonization in the host intestine contributed to the pathogenicity of P. donghuensis HYS. In addition, experiments using the worm mutants ZD101, KU4 and KU25 revealed a correlation between P. donghuensis HYS virulence and the TIR-1/SEK-1/PMK-1 pathways of the innate immune p38 MAPK pathway in C. elegans. In conclusion, these results reveal that the specific virulence gene cluster gtrA/B/II contributes to the unique pathogenicity of HYS compared with other pathogenic Pseudomonas, and that this process also involves C. elegans innate immunity. These findings significantly increase the available information about GtrA/GtrB/GtrII-based virulence mechanisms in the genus Pseudomonas.

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How to make a rodent giant: Genomic basis and tradeoffs of gigantism in the capybara, the world’s largest rodent

Molecular Biology and Evolution ◽

10.1093/molbev/msaa285 ◽

2020 ◽

Author(s):

Santiago Herrera-Álvarez ◽

Elinor Karlsson ◽

Oliver A Ryder ◽

Kerstin Lindblad-Toh ◽

Andrew J Crawford

Keyword(s):

Body Size ◽

Draft Genome ◽

Large Body ◽

Comparative Genomic ◽

Specific Gene ◽

Large Body Size ◽

Synonymous Mutations ◽

Intragenomic Conflict ◽

Genome Wide ◽

A Genome

Abstract Gigantism results when one lineage within a clade evolves extremely large body size relative to its small-bodied ancestors, a common phenomenon in animals. Theory predicts that the evolution of giants should be constrained by two tradeoffs. First, because body size is negatively correlated with population size, purifying selection is expected to be less efficient in species of large body size, leading to increased mutational load. Second, gigantism is achieved through generating a higher number of cells along with higher rates of cell proliferation, thus increasing the likelihood of cancer. To explore the genetic basis of gigantism in rodents and uncover genomic signatures of gigantism-related tradeoffs, we assembled a draft genome of the capybara (Hydrochoerus hydrochaeris), the world’s largest living rodent. We found that the genome-wide ratio of non-synonymous to synonymous mutations (ω) is elevated in the capybara relative to other rodents, likely caused by a generation-time effect and consistent with a nearly-neutral model of molecular evolution. A genome-wide scan for adaptive protein evolution in the capybara highlighted several genes controlling post-natal bone growth regulation and musculoskeletal development, which are relevant to anatomical and developmental modifications for an increase in overall body size. Capybara-specific gene-family expansions included a putative novel anticancer adaptation that involves T cell-mediated tumor suppression, offering a potential resolution to the increased cancer risk in this lineage. Our comparative genomic results uncovered the signature of an intragenomic conflict where the evolution of gigantism in the capybara involved selection on genes and pathways that are directly linked to cancer.

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SID-4/NCK-1 is important for dsRNA import in Caenorhabditis elegans

10.1101/702019 ◽

2019 ◽

Cited By ~ 1

Author(s):

Sonya Bhatia ◽

Craig P. Hunter

Keyword(s):

Temperature Effects ◽

Adaptor Protein ◽

Specific Gene ◽

Genetic Screens ◽

Rnai Silencing ◽

C Elegans ◽

Sensitivity Tests ◽

Systemic Rnai ◽

Signaling Components ◽

Additive Resistance

AbstractRNA interference (RNAi) is sequence-specific gene silencing triggered by double-stranded (ds)RNA. When dsRNA is expressed or introduced into one cell and is transported to and initiates RNAi in other cells, it is called systemic RNAi. Systemic RNAi is very efficient in C. elegans and genetic screens for systemic RNAi defective (Sid) mutants have identified RNA transporters (SID-1, SID-2 and SID-5) and a signaling protein (SID-3). Here we report that SID-4 is nck-1, a C. elegans NCK-like adaptor protein. sid-4 null mutations cause a weak, dosesensitive, systemic RNAi defect and can be effectively rescued by SID-4 expression in target tissues only, implying a role in dsRNA import. SID-4 and SID-3 (ACK-1 kinase) homologs interact in mammals and insects, suggesting they may function in a common signaling pathway, however, a sid-3; sid-4 double mutants showed additive resistance to RNAi, suggesting that these proteins likely interact with other signaling pathways as well. A bioinformatic screen coupled to RNAi sensitivity tests identified 23 additional signaling components with weak RNAi defective phenotypes. These observations suggest that environmental conditions may modulate systemic RNAi efficacy, and indeed, sid-3 and sid-4 are required for growth temperature effects on systemic RNAi silencing efficiency.

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Deficiency for Piwi results in transmission of a heritable stress that promotes longevity via DAF-16/Foxo

10.1101/326769 ◽

2018 ◽

Author(s):

Bree Heestand ◽

Matt Simon ◽

Stephen Frenk ◽

Shawn Ahmed

Keyword(s):

Germ Cell ◽

Germ Cells ◽

Stress Resistance ◽

Rnai Pathway ◽

Early Generation ◽

C Elegans ◽

Systemic Rnai ◽

Late Generation ◽

Cell Immortality ◽

F1 Cross

AbstractThe C. elegans Piwi Argonaute protein PRG-1 and associated piRNAs protect the genomes of germ cells by suppressing the expression of transposons and potentially deleterious foreign nucleic acids. Deficiency for prg-1 compromises germ cell immortality, resulting in normal fertility for many generations followed by progressively reduced fertility and ultimately sterility. The sterility phenotype of prg-1 mutants was recently shown to be a form of reproductive arrest, which implies that prg-1 mutants may become sterile in response to a form of heritable stress. The DAF-16 stress resistance and longevity factor can promote germ cell immortality of prg-1 mutants by activating a systemic RNAi pathway. We found that this RNAi pathway was not required for the somatic longevity function of DAF-16. Given that prg-1 mutant germ cells may transmit a form of heritable stress, we studied the somatic longevity of prg-1 mutant adults. We found that early generation prg-1 mutants had normal lifespans, but that late-generation adults that displayed reduced fertility or sterility were long lived. Germ cells of long-lived late-generation prg-1 mutants gave rise to F1 cross progeny that were heterozygous for prg-1, fertile and also long lived. However, in the absence of DAF-16, the heritable stress transmitted by prg-1 mutant germ cells was deleterious and caused lifespan to shorten. We conclude that deficiency for the genomic surveillance factor PRG-1/Piwi results in germ cells that transmit a heritable stress that promotes somatic longevity via DAF-16/Foxo, which could be relevant transgenerational regulationof aging.

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Antiviral RNA Interference against Orsay Virus Is neither Systemic nor Transgenerational in Caenorhabditis elegans

Journal of Virology ◽

10.1128/jvi.03664-14 ◽

2015 ◽

Vol 89 (23) ◽

pp. 12035-12046 ◽

Cited By ~ 26

Author(s):

Alyson Ashe ◽

Peter Sarkies ◽

Jérémie Le Pen ◽

Mélanie Tanguy ◽

Eric A. Miska

Keyword(s):

Caenorhabditis Elegans ◽

Virus Infection ◽

Viral Infection ◽

Rna Virus ◽

Rnai Pathway ◽

Content Type ◽

C Elegans ◽

Systemic Rnai ◽

Endogenous Role ◽

Orsay Virus

ABSTRACTAntiviral RNA-mediated silencing (RNA interference [RNAi]) acts as a powerful innate immunity defense in plants, invertebrates, and mammals. InCaenorhabditis elegans, RNAi is systemic; i.e., RNAi silencing signals can move between cells and tissues. Furthermore, RNAi effects can be inherited transgenerationally and may last for many generations. Neither the biological relevance of systemic RNAi nor transgenerational RNAi is currently understood. Here we examined the role of both pathways in the protection ofC. elegansfrom viral infection. We studied the Orsay virus, a positive-strand RNA virus related toNodaviridaeand the first and only virus known to infectC. elegans. Immunity to Orsay virus infection requires the RNAi pathway. Surprisingly, we found that genes required for systemic or transgenerational RNAi did not have a role in antiviral defense. Furthermore, we found that Orsay virus infection did not elicit a systemic RNAi response even when a target for RNAi was provided by using transgenes. Finally, we show that viral siRNAs, the effectors of RNAi, are not inherited to a level that provides any significant resistance to viral infection in the next generation. We conclude that systemic or transgenerational RNAi does not play a role in the defense against natural Orsay virus infection. Furthermore, our data suggest that there is a qualitative difference between experimental RNAi and antiviral RNAi. Our data are consistent with a model of systemic and transgenerational RNAi that requires a nuclear or germ line component that is lacking in almost all RNA virus infections.IMPORTANCESince its discovery inCaenorhabditis elegans, RNAi has proven a valuable scientific tool in many organisms. InC. elegans, exogenous RNAi spreads throughout the organism and can be passed between generations; however, there has been controversy as to the endogenous role(s) that the RNAi pathway plays. One endogenous role for which spreading both within the infected organism and between generations would be advantageous is a role in viral defense. In plants, antiviral RNAi is systemic and the spread of RNAi between cells provides protection against subsequent viral infection. Here we investigated this by using the only naturally occurring virus known to infectC. elegans, Orsay virus, and surprisingly found that, in contrast to the exogenous RNAi pathway, the antiviral RNAi response targeted against this virus does not spread systemically throughout the organism and cannot be passed between generations. These results suggest that there are differences between the two pathways that remain to be discovered.

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