scholarly journals Emergent RNA-RNA interactions can promote stability in a nascent phototrophic endosymbiosis

2021 ◽  
Author(s):  
Benjamin H Jenkins ◽  
Finlay Maguire ◽  
Guy Leonard ◽  
Joshua D Eaton ◽  
Steven West ◽  
...  
Keyword(s):  
Rna Processing ◽  
Rnai Pathway ◽  
Knock Down ◽  
Sequence Identity ◽  
Host Growth ◽  
Multiple Regions ◽  
Enforcement Mechanisms ◽  
Genetic Integration ◽  
Host Genes ◽  
Biological Organisms

Eukaryote-eukaryote endosymbiosis was responsible for the spread of photosynthetic organelles. Interaction stability is required for the metabolic and genetic integration that drives the establishment of new organelles, yet the mechanisms which act to stabilise nascent endosymbioses - between two fundamentally selfish biological organisms - are unclear. Theory suggests that enforcement mechanisms, which punish misbehaviour, may act to stabilise such interactions by resolving conflict. However, how such mechanisms can emerge in a nascent eukaryote-eukaryote endosymbiosis has yet to be explored. Here, we propose that endosymbiont-host RNA-RNA interactions, arising from digestion of endosymbionts, can result in a cost to host growth for breakdown of the endosymbiosis. Using the model nascent endosymbiosis, Paramecium bursaria - Chlorella spp., we demonstrate that this mechanism is dependent on the host RNA-interference (RNAi) pathway. We reveal through small RNA (sRNA) sequencing that endosymbiont-derived mRNA released upon endosymbiont digestion can be processed by the host RNAi system into 23-nt sRNA. We additionally identify multiple regions of shared sequence identity between endosymbiont and host mRNA, and demonstrate, through delivery of synthetic endosymbiont sRNA, that exposure to these regions can knock-down expression of complementary host genes, resulting in a cost to host growth. This process of host gene knock-down in response to endosymbiont-derived RNA processing by the host, which we term 'RNAi-collisions', represents a mechanism which can promote stability in a nascent eukaryote-eukaryote endosymbiosis. By imposing a cost for breakdown of the endosymbiosis, endosymbiont-host RNA-RNA interactions may drive maintenance of a symbiosis across fluctuating ecologies and symbiotic states.

scholarly journals Emergent RNA–RNA interactions can promote stability in a facultative phototrophic endosymbiosis

2021 ◽  
Vol 118 (38) ◽  
pp. e2108874118
Author(s):  
Benjamin H. Jenkins ◽  
Finlay Maguire ◽  
Guy Leonard ◽  
Joshua D. Eaton ◽  
Steven West ◽  
...  
Keyword(s):  
Small Rna ◽  
Rna Processing ◽  
Messenger Rna ◽  
Sequence Identity ◽  
Host Growth ◽  
Multiple Regions ◽  
Enforcement Mechanisms ◽  
Genetic Integration ◽  
Host Genes ◽  
Biological Organisms

Eukaryote–eukaryote endosymbiosis was responsible for the spread of chloroplast (plastid) organelles. Stability is required for the metabolic and genetic integration that drives the establishment of new organelles, yet the mechanisms that act to stabilize emergent endosymbioses—between two fundamentally selfish biological organisms—are unclear. Theory suggests that enforcement mechanisms, which punish misbehavior, may act to stabilize such interactions by resolving conflict. However, how such mechanisms can emerge in a facultative endosymbiosis has yet to be explored. Here, we propose that endosymbiont–host RNA–RNA interactions, arising from digestion of the endosymbiont population, can result in a cost to host growth for breakdown of the endosymbiosis. Using the model facultative endosymbiosis between Paramecium bursaria and Chlorella spp., we demonstrate that this mechanism is dependent on the host RNA-interference (RNAi) system. We reveal through small RNA (sRNA) sequencing that endosymbiont-derived messenger RNA (mRNA) released upon endosymbiont digestion can be processed by the host RNAi system into 23-nt sRNA. We predict multiple regions of shared sequence identity between endosymbiont and host mRNA, and demonstrate through delivery of synthetic endosymbiont sRNA that exposure to these regions can knock down expression of complementary host genes, resulting in a cost to host growth. This process of host gene knockdown in response to endosymbiont-derived RNA processing by host RNAi factors, which we term “RNAi collisions,” represents a mechanism that can promote stability in a facultative eukaryote–eukaryote endosymbiosis. Specifically, by imposing a cost for breakdown of the endosymbiosis, endosymbiont–host RNA–RNA interactions may drive maintenance of the symbiosis across fluctuating ecological conditions.

scholarly journals Characterisation of the RNA-interference pathway as a Tool for Genetics in the Nascent Phototrophic Endosymbiosis, Paramecium bursaria

2020 ◽  
Author(s):  
Benjamin H. Jenkins ◽  
Finlay Maguire ◽  
Guy Leonard ◽  
Joshua D. Eaton ◽  
Steven West ◽  
...  
Keyword(s):  
Rna Interference ◽  
Genetic Basis ◽  
Paramecium Bursaria ◽  
Rnai Pathway ◽  
Knock Down ◽  
Protein Encoding ◽  
Host Growth ◽  
Rna Pathways ◽  
Si Rna ◽  
Encoding Genes

ABSTRACTEndosymbiosis was fundamental for the evolution of eukaryotic complexity. Endosymbiotic interactions can be dissected through forward and reverse-genetic experiments, such as RNA-interference (RNAi). However, distinguishing small (s)RNA pathways in a eukaryote-eukaryote endosymbiotic interaction is challenging. Here, we investigate the repertoire of RNAi pathway protein-encoding genes in the model nascent endosymbiotic system, Paramecium bursaria–Chlorella spp. Using comparative genomics and transcriptomics supported by phylogentics, we identify essential proteome components of the small interfering (si)RNA, scan (scn)RNA, and internal eliminated sequence (ies)RNA pathways. Our analyses reveal that copies of these components have been retained throughout successive whole genome duplication (WGD) events in the Paramecium clade. We then validate feeding-induced siRNA-based RNAi in P. bursaria via knock-down of the splicing factor, u2af1, which we show to be crucial to host growth. Finally, using simultaneous knock-down paradox controls to rescue the effect u2af1 knock-down, we demonstrate that feeding-induced RNAi in P. bursaria is dependent upon a core pathway of host-encoded Dcr1, Piwi and Pds1 components. Our experiments confirm the presence of a functional, host-derived RNAi pathway in P. bursaria that generates 23-nt siRNA, validating use of the P. bursaria-Chlorella spp. system to investigate the genetic basis of a nascent endosymbiosis.

scholarly journals Characterization of the RNA-interference pathway as a tool for reverse genetic analysis in the nascent phototrophic endosymbiosis, Paramecium bursaria

2021 ◽  
Vol 8 (4) ◽  
Author(s):  
Benjamin H. Jenkins ◽  
Finlay Maguire ◽  
Guy Leonard ◽  
Joshua D. Eaton ◽  
Steven West ◽  
...  
Keyword(s):  
Rna Interference ◽  
Paramecium Bursaria ◽  
Rnai Pathway ◽  
Reverse Genetic ◽  
Knock Down ◽  
Protein Encoding ◽  
Host Growth ◽  
Rna Pathways ◽  
Si Rna

Endosymbiosis was fundamental for the evolution of eukaryotic complexity. Endosymbiotic interactions can be dissected through forward- and reverse-genetic experiments, such as RNA-interference (RNAi). However, distinguishing small (s)RNA pathways in a eukaryote–eukaryote endosymbiotic interaction is challenging. Here, we investigate the repertoire of RNAi pathway protein-encoding genes in the model nascent endosymbiotic system, Paramecium bursaria–Chlorella spp. Using comparative genomics and transcriptomics supported by phylogenetics, we identify essential proteome components of the small interfering (si)RNA, scan (scn)RNA and internal eliminated sequence (ies)RNA pathways. Our analyses reveal that copies of these components have been retained throughout successive whole genome duplication (WGD) events in the Paramecium clade. We validate feeding-induced siRNA-based RNAi in P. bursaria via knock-down of the splicing factor, u2af1 , which we show to be crucial to host growth. Finally, using simultaneous knock-down ‘paradox’ controls to rescue the effect of u2af1 knock-down, we demonstrate that feeding-induced RNAi in P. bursaria is dependent upon a core pathway of host-encoded Dcr1 , Piwi and Pds1 components. Our experiments confirm the presence of a functional, host-derived RNAi pathway in P. bursaria that generates 23-nt siRNA, validating the use of the P. bursaria – Chlorella spp. system to investigate the genetic basis of a nascent endosymbiosis.

scholarly journals Short regions of sequence identity between the genomes of human and rodent parvoviruses and their respective hosts occur within host genes for the cytoskeleton, cell adhesion and Wnt signalling

2006 ◽  
Vol 87 (12) ◽  
pp. 3567-3575 ◽  
Author(s):  
Jonathan R. Kerr ◽  
Nicola Boschetti
Keyword(s):  
Cell Adhesion ◽  
Parvovirus B19 ◽  
Prototype Strain ◽  
Wnt Signalling ◽  
Host Genome ◽  
Virus Species ◽  
Genome Sequences ◽  
Sequence Identity ◽  
Intergenic Regions ◽  
Host Genes

Our understanding of the mechanism(s) of pathogenesis and persistence of vertebrate parvoviruses remains incomplete. With the recent availability of the complete genome sequences of human, rat and mouse, and the ability to search these sequences and to locate matches to exact genomic regions, further insight into the interaction of parvoviruses with their human and rodent hosts is possible. To determine the extent and nature of sequence identity between candidate parvoviruses and their respective hosts, blast searches of the genome sequences of adeno-associated virus, parvovirus B19, mouse parvovirus, the prototype strain and immunosuppressant variant of minute virus of mouse, Kilham rat virus and rat parvovirus were performed against the genome(s) of their respective hosts (human, rat and mouse) using the resources of the NCBI and the Celera Discovery System. Regions of identity and similarity were mapped to their precise location in their particular host genome. For each virus, between one and 12 identical regions were found. Each identical region was 17–26 nt and was generally found at multiple sites within the particular host genome. These identical regions were predominantly located in non-coding regions of particular host genes and in intergenic regions. The ontology of host genes in which identical regions were found for each of the nine virus–host interactions highlighted several pathways/processes, including the cytoskeleton, cell adhesion and Wnt signalling. Within each virus species, these homologous regions were highly conserved (100 % identity in 16 out of 23 alignments where more than one sequence was available). All of these aspects suggest a particular advantage to the viruses of the presence of these sequences.

scholarly journals Shrimp Parvovirus Circular DNA Fragments Arise From Both Endogenous Viral Elements and the Infecting Virus

2021 ◽  
Vol 12 ◽  
Author(s):  
Suparat Taengchaiyaphum ◽  
Phasini Buathongkam ◽  
Suchitraporn Sukthaworn ◽  
Prapatsorn Wongkhaluang ◽  
Kallaya Sritunyalucksana ◽  
...  
Keyword(s):  
Penaeus Monodon ◽  
Rnai Pathway ◽  
Breeding Programs ◽  
Sequence Identity ◽  
Viral Copy ◽  
Copy Dna ◽  
Endogenous Viral Elements ◽  
Next Generation Sequencing Ngs ◽  
Interfering Rna ◽  
Generation Sequencing

Some insects use endogenous reverse transcriptase (RT) to make variable viral copy DNA (vcDNA) fragments from viral RNA in linear (lvcDNA) and circular (cvcDNA) forms. The latter form is easy to extract selectively. The vcDNA produces small interfering RNA (siRNA) variants that inhibit viral replication via the RNA interference (RNAi) pathway. The vcDNA is also autonomously inserted into the host genome as endogenous viral elements (EVE) that can also result in RNAi. We hypothesized that similar mechanisms occurred in shrimp. We used the insect methods to extract circular viral copy DNA (cvcDNA) from the giant tiger shrimp (Penaeus monodon) infected with a virus originally named infectious hypodermal and hematopoietic necrosis virus (IHHNV). Simultaneous injection of the extracted cvcDNA plus IHHNV into whiteleg shrimp (Penaeus vannamei) resulted in a significant reduction in IHHNV replication when compared to shrimp injected with IHHNV only. Next generation sequencing (NGS) revealed that the extract contained a mixture of two general IHHNV-cvcDNA types. One showed 98 to 99% sequence identity to GenBank record AF218266 from an extant type of infectious IHHNV. The other type showed 98% sequence identity to GenBank record DQ228358, an EVE formerly called non-infectious IHHNV. The startling discovery that EVE could also give rise to cvcDNA revealed that cvcDNA provided an easy means to identify and characterize EVE in shrimp and perhaps other organisms. These studies open the way for identification, characterization and use of protective cvcDNA as a potential shrimp vaccine and as a tool to identify, characterize and select naturally protective EVE to improve shrimp tolerance to homologous viruses in breeding programs.

scholarly journals Shrimp parvovirus circular DNA fragments arise from both endogenous viral elements (EVE) and the infecting virus

2021 ◽  
Author(s):  
Suparat Taengchaiyaphum ◽  
Phasini Buathongkam ◽  
Suchitraporn Sukthaworn ◽  
Prapatsorn Wongkhaluang ◽  
Kallaya Sritunyalucksana ◽  
...  
Keyword(s):  
Penaeus Monodon ◽  
Rnai Pathway ◽  
Breeding Programs ◽  
Sequence Identity ◽  
Link Type ◽  
Viral Copy ◽  
Copy Dna ◽  
Endogenous Viral Elements ◽  
Next Generation Sequencing Ngs ◽  
Interfering Rna

Some insects use endogenous reverse transcriptase (RT) to make variable linear and circular viral copy DNA (vcDNA) fragments from viral RNA. The vcDNA produces small interfering RNA (siRNA) variants that inhibit viral replication via the RNA interference (RNAi) pathway. The vcDNA is also autonomously inserted into the host genome as endogenous viral elements (EVE) that can also result in RNAi. We hypothesized that similar mechanisms occurred in shrimp. We used the insect methods to extract circular viral copy DNA (cvcDNA) from the giant tiger shrimp (Penaeus monodon) infected with a virus originally named infectious hypodermal and hematopoietic necrosis virus (IHHNV). Simultaneous injection of the extracted cvcDNA plus IHHNV into whiteleg shrimp (Penaeus vannamei) resulted in a significant reduction in IHHNV replication when compared to shrimp injected with IHHNV only. Next generation sequencing (NGS) revealed that the extract contained a mixture of two general IHHNV-cvcDNA types. One showed 98 to 99% sequence identity to GenBank record AF218266 from an extant type of infectious IHHNV. The other type showed 98% sequence identity to GenBank record DQ228358, an EVE formerly called non-infectious IHHNV. The startling discovery that EVE could also give rise to cvcDNA revealed that cvcDNA provided an easy means to identify and characterize EVE in shrimp and perhaps other organisms. These studies open the way for identification, characterization and use of protective cvcDNA as a potential shrimp vaccine and as a tool to identify, characterize and select naturally protective EVE to improve shrimp tolerance to homologous viruses in breeding programs.

273: Knock-Down of BCL-2 By Antisense Oligodeoxynucleotides Induces Radiosensitization and Inhibition of Angiogenesis

2007 ◽  
Vol 177 (4S) ◽  
pp. 91-92
Author(s):  
Satoshi Anai ◽  
Yoshihisa Sakai ◽  
Steve Goodison ◽  
Kathleen Shiverick ◽  
Bob Brown ◽  
...  
Keyword(s):  
Antisense Oligodeoxynucleotides ◽  
Knock Down ◽  
Inhibition Of Angiogenesis

Schutz vor Insekten

2005 ◽  
Vol 62 (11) ◽  
pp. 713-718 ◽  
Author(s):  
Rudin
Keyword(s):  
Vitamin B ◽  
Eucalyptus Citriodora ◽  
Knock Down

Erfolgreicher Schutz gegen Stiche von blutsaugenden Insekten und Zecken bedingt die konsequente Anwendung geeigneter Maßnahmen. Eine eventuell notwendige Chemoprophylaxe wird dadurch nie ersetzt. Die Umstände, unter denen der Schutz erreicht werden soll, bestimmen die Kombination der zu treffenden Maßnahmen. Von Wohnräumen kann man Insekten mit Mückengittern oder -gaze an Fenstern und Türen oder mittels Klimaanlagen fernhalten. Beim Schlafen kann man sich mit einem Moskitonetz schützen. Diese Maßnahmen können bei Bedarf durch Insektizide ergänzt oder unterstützt werden. Meistens kommen synthetische Pyrethroide entweder als «knock down»-Sprays oder elektroverdampft für die Behandlung von Räumen oder als Imprägnierungsmittel von Netzen und Gittern zum Einsatz. Wenn ein Kontakt nicht durch die Wahl von Aufenthaltsort und -zeit vermeidbar ist, werden außer Haus zum Schutz vor Stichen geeignete Kleidung sowie Repellentien eingesetzt. Kleider sollen möglichst viel Körperfläche bedecken, aus festem Gewebe, nicht eng anliegend und von heller Farbe sein. Eine zusätzliche Behandlung mit Insektiziden ist vorteilhaft. Repellentien werden direkt auf die Haut appliziert. Diethylmethylbenzamin (DEET) zeigt seit vielen Jahren eine verlässliche Wirkung. Ebenfalls verbreitete synthetische Wirkstoffe sind Bayrepel® und IR3535. Sie weisen ein noch etwas geringeres Nebenwirkungsrisiko auf, nachteilig ist jedoch die schwächere Wirkung. Von den pflanzlichen Produkten sind die mit einem Extrakt aus Eucalyptus citriodora die am besten wirksamen. Schwächere Produkte schützen Personen, die für Mücken speziell attraktiv sind, nur ungenügend. Völlig nutzlos sind auf Arm-, Halsbänder oder Kleber aufgetragene Repellentien, sowie Ultraschallgeräte, UV-Lichtfallen oder die Einnahme von Vitamin B1 oder Knoblauch.

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