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 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 DNA Damage–Induced BARD1 Phosphorylation Is Critical for the Inhibition of Messenger RNA Processing by BRCA1/BARD1 Complex

2006 ◽  
Vol 66 (9) ◽  
pp. 4561-4565 ◽  
Author(s):  
Ho-Shik Kim ◽  
Hongjie Li ◽  
Murat Cevher ◽  
Alissa Parmelee ◽  
Danae Fonseca ◽  
...  
Keyword(s):  
Dna Damage ◽  
Rna Processing ◽  
Messenger Rna

scholarly journals Pre-Messenger RNA Processing Factors in the Drosophila Genome

2000 ◽  
Vol 150 (2) ◽  
pp. F37-F44 ◽  
Author(s):  
Stephen M. Mount ◽  
Helen K. Salz
Keyword(s):  
Rna Processing ◽  
Messenger Rna ◽  
Drosophila Genome ◽  
Processing Factors

Small RNA and transcriptome sequencing of a symptomatic peony plant reveals mixed infections with novel viruses

Plant Disease ◽  
2021 ◽  
Author(s):  
Anning Jia ◽  
Chenge Yan ◽  
Hang Yin ◽  
Rui Sun ◽  
Fei Xia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Viral Infections ◽  
Triple Gene Block ◽  
Field Investigation ◽  
Mixed Infections ◽  
Species Classification ◽  
Gene Block ◽  
Sequence Identity

To identify the viruses in tree peony plants associated with the symptoms of yellowing, leaf rolling, stunted growth, and decline, high-throughput sequencing of small RNA and mRNA was conducted from a single symptomatic plant. Bioinformatic analyses and reconstruction of viral genomes indicated mixed viral infections involving cycas necrotic stunt virus (CNSV), apple stem grooving virus (ASGV), lychnis mottle virus (LycMoV), grapevine line pattern virus (GLPV), and three new viruses designated as peony yellowing-associated citrivirus (PYaCV, Citrivirus in Betaflexiviridae), peony betaflexivirus 1 (PeV1, unclassified in Betaflexiviridae), and peony leafroll-associated virus (PLRaV, Ampelovirus in Closteroviridae). PYaCV was 8,666 nucleaotides (nt) in length, comprising three open reading frames (ORFs) and shared 63.8–75.9% nucleotide sequence identity with citrus leaf blotch virus (CLBV) isolates. However, the ORF encoding the replication-associated protein (REP) shared 57% and 52% sequence identities at the nt and amino acid (aa) level, respectively, with other reported CLBV isolates, which were below the criterion for species classification within the family Betaflexiviridae. Recombination analysis identified putative recombination sites in PYaCV, which originated from CLBV. PeV1, only identified from the transcriptome data, was 8,124 nt in length with five ORFs encoding the REP (ORF1), triple gene block (TGB, ORF2–4) and coat protein (CP, ORF5) proteins. Phylogenetic analysis and sequence comparison showed that PeV1 clustered with an unassigned member, the garlic yellow mosaic-associated virus (GYMaV) within the Betaflexiviridae family, into a separate clade. Partial genome sequence analysis of PLRaV (12,545 nt) showed it contained seven ORFs encoding the partial polyprotein 1a, the RNA-dependent RNA polymerase (RdRp), two small hydrophobic proteins p11 and p6, HSP70h, p55, and a CP duplicate, which shared low aa sequence identity with Closteroviridae family members. Phylogenetic analysis based on the aa sequences of RdRp or HSP70h indicated that PLRaV clustered with grapevine leafroll-associated virus 1 (GLRaV-1) and GLRaV-13 in the Ampelovirus genus. Field investigation confirmed the wide distribution of these viruses, causing mixed infections of peony plants in Beijing.

scholarly journals A dual reporter approach to quantify defects in messenger RNA processing

2009 ◽  
Vol 395 (2) ◽  
pp. 237-243 ◽  
Author(s):  
Ayan Banerjee ◽  
Mimi C. Sammarco ◽  
Scott Ditch ◽  
Ed Grabczyk
Keyword(s):  
Rna Processing ◽  
Messenger Rna ◽  
Dual Reporter

Messenger RNA Processing in Eukaryotes

2013 ◽  
pp. 59-64
Author(s):  
K. Potter ◽  
N. Cremona ◽  
J.A. Wise
Keyword(s):  
Rna Processing ◽  
Messenger Rna

scholarly journals Feedback regulation of small RNA processing by the cleavage product

RNA Biology ◽  
2019 ◽  
Vol 16 (8) ◽  
pp. 1055-1065 ◽  
Author(s):  
Svetlana Durica-Mitic ◽  
Boris Görke
Keyword(s):  
Small Rna ◽  
Rna Processing ◽  
Feedback Regulation ◽  
Cleavage Product

scholarly journals An improved method of constructing degradome library suitable for sequencing using Illumina platform

Plant Methods ◽  
2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Yong-Fang Li ◽  
Miao Zhao ◽  
Menglei Wang ◽  
Junqiang Guo ◽  
Li Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Small Rna ◽  
Messenger Rna ◽  
High Throughput Sequencing ◽  
Mirna Family ◽  
Mirna Biogenesis ◽  
Improved Method ◽  
Illumina Platform ◽  
Transcriptional Gene Regulation ◽  
Small Rna Library

Abstract Background Post-transcriptional gene regulation is one of the critical layers of overall gene expression programs and microRNAs (miRNAs) play an indispensable role in this process by guiding cleavage on the messenger RNA targets. The transcriptome-wide cleavages on the target transcripts can be identified by analyzing the degradome or PARE or GMUCT libraries. However, high-throughput sequencing of PARE or degradome libraries using Illumina platform, a widely used platform, is not so straightforward. Moreover, the currently used degradome or PARE methods utilize MmeI restriction site in the 5′ RNA adapter and the resulting fragments are only 20-nt long, which often poses difficulty in distinguishing between the members of the same target gene family or distinguishing miRNA biogenesis intermediates from the primary miRNA transcripts belonging to the same miRNA family. Consequently, developing a method which can generate longer fragments from the PARE or degradome libraries which can also be sequenced easily using Illumina platform is ideal. Results In this protocol, 3′ end of the 5′RNA adaptor of TruSeq small RNA library is modified by introducing EcoP15I recognition site. Correspondingly, the double-strand DNA (dsDNA) adaptor sequence is also modified to suit with the ends generated by the restriction enzyme EcoP15I. These modifications allow amplification of the degradome library by primer pairs used for small RNA library preparation, thus amenable for sequencing using Illumina platform, like small RNA library. Conclusions Degradome library generated using this improved protocol can be sequenced easily using Illumina platform, and the resulting tag length is ~ 27-nt, which is longer than the MmeI generated fragment (20-nt) that can facilitate better accuracy in validating target transcripts belonging to the same gene family or distinguishing miRNA biogenesis intermediates of the same miRNA family. Furthermore, this improved method allows pooling and sequencing degradome libraries and small RNA libraries simultaneously using Illumina platform.

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