scholarly journals Lost and Found: Piwi and Argonaute Pathways in Flatworms

2021 ◽  
Vol 11 ◽  
Author(s):  
Santiago Fontenla ◽  
Gabriel Rinaldi ◽  
Jose F. Tort
Keyword(s):  
Small Rna ◽  
Specific Class ◽  
Free Living ◽  
Parasitic Species ◽  
Argonaute Proteins ◽  
Wide Range ◽  
Invertebrate Animals ◽  
Living Species ◽  
Rna Pathways ◽  
Key Residues

Platyhelminthes comprise one of the major phyla of invertebrate animals, inhabiting a wide range of ecosystems, and one of the most successful in adapting to parasitic life. Small non-coding RNAs have been implicated in regulating complex developmental transitions in model parasitic species. Notably, parasitic flatworms have lost Piwi RNA pathways but gained a novel Argonaute gene. Herein, we analyzed, contrasted and compared the conservation of small RNA pathways among several free-living species (a paraphyletic group traditionally known as ‘turbellarians’) and parasitic species (organized in the monophyletic clade Neodermata) to disentangle possible adaptations during the transition to parasitism. Our findings showed that complete miRNA and RNAi pathways are present in all analyzed free-living flatworms. Remarkably, whilst all ‘turbellarians’ have Piwi proteins, these were lost in parasitic Neodermantans. Moreover, two clusters of Piwi class Argonaute genes are present in all ‘turbellarians’. Interestingly, we identified a divergent Piwi class Argonaute in free living flatworms exclusively, which we named ‘Fliwi’. In addition, other key proteins of the Piwi pathways were conserved in ‘turbellarians’, while none of them were detected in Neodermatans. Besides Piwi and the canonical Argonaute proteins, a flatworm-specific class of Argonautes (FL-Ago) was identified in the analyzed species confirming its ancestrallity to all Platyhelminthes. Remarkably, this clade was expanded in parasitic Neodermatans, but not in free-living species. These phyla-specific Argonautes showed lower sequence conservation compared to other Argonaute proteins, suggesting that they might have been subjected to high evolutionary rates. However, key residues involved in the interaction with the small RNA and mRNA cleavage in the canonical Argonautes were more conserved in the FL-Agos than in the Piwi Argonautes. Whether this is related to specialized functions and adaptations to parasitism in Neodermatans remains unclear. In conclusion, differences detected in gene conservation, sequence and structure of the Argonaute family suggest tentative biological and evolutionary diversifications that are unique to Platyhelminthes. The remarkable divergencies in the small RNA pathways between free-living and parasitic flatworms indicate that they may have been involved in the adaptation to parasitism of Neodermatans.

scholarly journals Protease-mediated processing of Argonaute proteins controls small RNA association

2020 ◽  
Author(s):  
Rajani Kanth Gudipati ◽  
Kathrin Braun ◽  
Foivos Gypas ◽  
Daniel Hess ◽  
Jan Schreier ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Proteolytic Processing ◽  
Genome Integrity ◽  
Wild Type ◽  
Selfish Genetic Elements ◽  
Argonaute Proteins ◽  
Processing Activity ◽  
Rna Pathways

SummarySmall RNA pathways defend the germlines of animals against selfish genetic elements and help to maintain genomic integrity. At the same time, their activity needs to be well-controlled to prevent silencing of ‘self’ genes. Here, we reveal a proteolytic mechanism that controls endogenous small interfering (22G) RNA activity in the Caenorhabditis elegans germline to protect genome integrity and maintain fertility. We find that WAGO-1 and WAGO-3 Argonaute (Ago) proteins are matured through proteolytic processing of their unusually proline-rich N-termini. In the absence of DPF-3, a P-granule-localized N-terminal dipeptidase orthologous to mammalian DPP8/9, processing fails, causing a change of identity of 22G RNAs bound to these WAGO proteins. Desilencing of repeat- and transposon-derived transcripts, DNA damage and acute sterility ensue. These phenotypes are recapitulated when WAGO-1 and WAGO-3 are rendered resistant to DFP-3-mediated processing, identifying them as critical substrates of DPF-3. We conclude that N-terminal processing of Ago proteins regulates their activity and promotes discrimination of self from non-self by ensuring association with the proper complement of small RNAs.Graphical Abstract: The role of DPF-3 in the fertility of the animalsIn wild type animals, the WAGO-1 and WAGO-3 Argonaute proteins are produced as immature pro-proteins with N-termini (N) that are unusually rich in prolines (P). N-terminal processing by DPF-3 is required for loading of the proper small RNA cargo and stabilization of WAGO-3. Accordingly, loss of this processing activity causes desilencing of transposable elements (TE), cell death and sterility.

scholarly journals GTSF-1 is required for the formation of a functional RNA-dependent RNA Polymerase complex in C. elegans

2018 ◽  
Author(s):  
Miguel Vasconcelos Almeida ◽  
Sabrina Dietz ◽  
Stefan Redl ◽  
Emil Karaulanov ◽  
Andrea Hildebrandt ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Gene Silencing ◽  
Small Rna ◽  
Small Rnas ◽  
Zinc Fingers ◽  
Specific Factor ◽  
Rna Dependent Rna Polymerase ◽  
C Elegans ◽  
Argonaute Proteins ◽  
Rna Pathways

AbstractIn every domain of life, Argonaute proteins and their associated small RNAs regulate gene expression. Despite great conservation of Argonaute proteins throughout evolution, many proteins acting in small RNA pathways are not widely conserved. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured, acidic C-terminal tail, are conserved in animals and act in small RNA pathways. In fly and mouse, they are required for fertility and have been shown to interact with Piwi clade Argonautes. We identified T06A10.3 as the Caenorhabditis elegans Gtsf1 homolog and named it gtsf-1. Given its conserved nature and roles in Piwi-mediated gene silencing, we sought out to characterize GTSF-1 in the context of the small RNA pathways of C. elegans. Like its homologs, GTSF-1 is required for normal fertility. Surprisingly, we report that GTSF-1 is not required for Piwi-mediated gene silencing. Instead, gtsf-1 mutants show strong depletion of a class of endogenous small RNAs, known as 26G-RNAs, and fully phenocopy mutants lacking RRF-3, the RNA-dependent RNA Polymerase that synthesizes 26G-RNAs. We show, both in vivo and in vitro, that GTSF-1 specifically and robustly interacts with RRF-3 via its tandem CHHC zinc fingers. Furthermore, we demonstrate that GTSF-1 is required for the assembly of a larger RRF-3 and DCR-1-containing complex, also known as ERIC, thereby allowing for 26G-RNA generation. We propose that GTSF-1 homologs may similarly act to drive the assembly of larger complexes that subsequently act in small RNA production and/or in imposing small RNA-mediated silencing activities.

scholarly journals Plasmids encode niche-specific traits in Lactobacillaceae

2020 ◽  
Author(s):  
Dimple Davray ◽  
Dipti Deo ◽  
Ram Kulkarni
Keyword(s):  
Gc Content ◽  
Nucleotide Sequences ◽  
Ecological Niches ◽  
Comparative Genomic ◽  
Fermented Foods ◽  
Probiotic Properties ◽  
Genome Sequences ◽  
Free Living ◽  
Wide Range ◽  
Living Species

AbstractThe species of family Lactobacillaceae are found in highly diverse environments and play an important role in fermented foods and probiotic products. Many of these species have been individually reported to harbor plasmids that encode important genes. In this study, we performed comparative genomic analysis of the publically available data of 512 plasmids from 282 strains represented by 51 species of this family and correlated the genomic features of plasmids with the ecological niches in which these species are found. Two-third of the species had at least one plasmid-harboring strain. Plasmid abundance and GC content were significantly lower in the vertebrate-adapted species as compared to the nomadic and free-living species. Hierarchical clustering (HCL) highlighted the distinct nature of plasmids from the nomadic and free-living species than those from the vertebrate-adapted species. EggNOG assisted functional annotation revealed that genes associated with transposition, conjugation, DNA repair and recombination, exopolysaccharide production, metal ion transport, toxin-antitoxin system, and stress tolerance were significantly enriched on the plasmids of the nomadic and in some cases nomadic and free-living species. On the other hand, genes related to anaerobic metabolism, ABC transporters, and major facilitator superfamily were found to be overrepresented on the plasmids of the vertebrate-adapted species. These genomic signatures are correlated to the comparatively nutrient-depleted, stressful and dynamic environments of nomadic and free-living species and nutrient-rich and anaerobic environments of the vertebrate-adapted species. Thus, these results indicate the contribution of the plasmids in the adaptation of lactobacilli to the respective habitats. This study also underlines the potential application of these plasmids in improving the technological and probiotic properties of lactic acid bacteria.Impact statementThe bacteria of the family Lactobacillaceae are present in the wide range of habitats and play an important role in human health, fermented foods and chemical industries. A few studies have demonstrated the presence of plasmids in the individual strains of Lactobacillaceae species encoding various traits. Extensive data of genome sequences of the lactobacilli are becoming available; however, no comprehensive analysis of the plasmid-encoded genes and determining their biological relevance across lactobacilli has been undertaken at a larger scale. In this study, we explored the genomic content of 512 plasmids of Lactobacillaceae species and correlated it to the three types of these species according to their ecological niches – vertebrate-adapted, free-living and nomadic. Comparatively lower plasmid abundance and GC content in the vertebrate-adapted species could be correlated to the presence of these species in the nutrient-rich environment. The genomic content of the plasmids was consistent with the respective lifestyle adopted by lactobacilli suggesting that the plasmids might enhance the niche-specific fitness of the strains. The plethora of important genes present on the plasmids can also make them a highly useful tool in improving the probiotic, technological and food-related properties of lactobacilli.Data summaryNucleotide sequences of plasmids of Lactobacillus strains for which complete genome sequences were available were retrieved from the NCBI genome [https://www.ncbi.nlm.nih.gov/genome] and PATRIC 3.5.41 databases on 31st March 2019. The dataset includes 512 nucleotide sequences of plasmids of 282 strains belonging to genus Lactobacillus before its reclassification into several genera (1). Details of the plasmids have been given in Table S1.

Nematology: Advances and Perspectives, Vol. 1, Nematode Morphology, Physiology and Ecology. By Z. X. Chen, S. Y. Chen and D. W. Dickson, pp. 656. International CABI Publishing, UK, 2004. ISBN 0 85199 645. £85.00 (US$150.00).

Parasitology ◽  
2005 ◽  
Vol 131 (3) ◽  
pp. 435-436
Author(s):  
JERZY M. BEHNKE
Keyword(s):  
The Other ◽  
Iron Curtain ◽  
Free Living ◽  
Cabi Publishing ◽  
Parasitic Species ◽  
Research Institutes ◽  
Living Species ◽  
Crop Research ◽  
Plant Parasitic

As a zoologist, I have never really understood why those of us who study nematodes continue to partition ourselves into at least two distinct camps, one of which works on the plant-parasitic and free-living species, and the other primarily on animal-parasitic species. And I suspect that nematodes themselves are equally puzzled by this segregation of their ardent scholars. Historically, of course, plant nematologists aggregated in crop research and botany departments, whereas the animal nematologists were stationed in livestock, veterinary, medical and zoological departments of research institutes and universities. I found much of interest in NematologyVol. 1, but I was left with the impression that, whilst the ‘iron curtain’ was beginning to tumble, it still had a long way to fall. We have not yet reached a stage where nematodes as distinct organisms, whatever their niche, take priority in our thinking. But I race ahead. Let us retrace and begin with the details of this volume.

scholarly journals Protease-mediated processing of Argonaute proteins controls small RNA association

2021 ◽  
Author(s):  
Rajani Kanth Gudipati ◽  
Kathrin Braun ◽  
Foivos Gypas ◽  
Daniel Hess ◽  
Jan Schreier ◽  
...  
Keyword(s):  
Small Rna ◽  
Argonaute Proteins

scholarly journals Misinformation tactics protect rare birds from problem predators

2021 ◽  
Vol 7 (11) ◽  
pp. eabe4164
Author(s):  
Grant L. Norbury ◽  
Catherine J. Price ◽  
M. Cecilia Latham ◽  
Samantha J. Brown ◽  
A. David M. Latham ◽  
...  
Keyword(s):  
Decision Making ◽  
Threatened Species ◽  
Prey Availability ◽  
Free Living ◽  
Bird Populations ◽  
New Information ◽  
Mammalian Predators ◽  
Decision Making Processes ◽  
Living Species ◽  
Information Reliability

Efficient decision-making integrates previous experience with new information. Tactical use of misinformation can alter choice in humans. Whether misinformation affects decision-making in other free-living species, including problem species, is unknown. Here, we show that sensory misinformation tactics can reduce the impacts of predators on vulnerable bird populations as effectively as lethal control. We repeatedly exposed invasive mammalian predators to unprofitable bird odors for 5 weeks before native shorebirds arrived for nesting and for 8 weeks thereafter. Chick production increased 1.7-fold at odor-treated sites over 25 to 35 days, with doubled or tripled odds of successful hatching, resulting in a 127% increase in modeled population size in 25 years. We demonstrate that decision-making processes that respond to changes in information reliability are vulnerable to tactical manipulation by misinformation. Altering perceptions of prey availability offers an innovative, nonlethal approach to managing problem predators and improving conservation outcomes for threatened species.

scholarly journals Nematode Hsp90: highly conserved but functionally diverse

Parasitology ◽  
2014 ◽  
Vol 141 (9) ◽  
pp. 1203-1215 ◽  
Author(s):  
VICTORIA GILLAN ◽  
EILEEN DEVANEY
Keyword(s):  
Life Cycle ◽  
Heat Shock Protein 90 ◽  
Ecological Niches ◽  
Actual Number ◽  
Host Organism ◽  
Free Living ◽  
Parasitic Species ◽  
Free Living Nematode ◽  
Functionally Diverse

SUMMARYNematodes are amongst the most successful and abundant organisms on the planet with approximately 30 000 species described, although the actual number of species is estimated to be one million or more. Despite sharing a relatively simple and invariant body plan, there is considerable diversity within the phylum. Nematodes have evolved to colonize most ecological niches, and can be free-living or can parasitize plants or animals to the detriment of the host organism. In this review we consider the role of heat shock protein 90 (Hsp90) in the nematode life cycle. We describe studies on Hsp90 in the free-living nematode Caenorhabditis elegans and comparative work on the parasitic species Brugia pahangi, and consider whether a dependence upon Hsp90 can be exploited for the control of parasitic species.

Arthropods in the nests of lesser spotted eagle (Aquila pomarina)

Biologia ◽  
2009 ◽  
Vol 64 (5) ◽  
Author(s):  
Ján Krištofík ◽  
Peter Mašán ◽  
Zbyšek Šustek ◽  
Dušan Karaska
Keyword(s):  
Trophic Group ◽  
Trophic Groups ◽  
Significant Component ◽  
Free Living ◽  
Parasitic Species ◽  
Number Of Species ◽  
Aquila Pomarina ◽  
Investigation Period ◽  
First Time

AbstractIn 2001–2007, altogether 57 nests of lesser spotted eagle were collected in the Orava region in northwestern Slovakia and four groups of arthropods were extracted from them. Richest in number of species and individuals were mites (23 species, 17,500 ind.), followed by beetles (12 species, 725 ind.), whereas pseudoscorpions were represented only by Pselaphochernes scorpioides (39 ind.) and fleas by Ceratophyllus garei (3 ind.). Unlike nests of other birds, free-living mites predominated in the nests fauna (83% of individuals), followed by nidicolous species with more or less free relationship to the nests, while parasitic species represented only a negligible part of the fauna. For the first time we observed phoresy of Nenteria pandioni, a specific and abundant mite in the eagles’ nests, on the nidicolous staphylinid Haploglossa puncticollis. The beetle fauna in the nests was much poorer than in nests of other birds. The predatory H. puncticollis was dominant in the nests (83%) and occurred continuously during the whole investigation period. Other beetles, even the widely distributed nidicols such as the histerid Gnathoncus buyssoni, were found rarely in nests. Predators were also the only abundant trophic group of beetles in the nests, while other trophic groups of beetles abundantly co-occur in nests of majority of other birds. The occurrence of all beetles was very unevenly distributed during the investigation period, but was positively correlated with occurrence of mites. The relatively low number of species and individuals of mites and beetles in the lesser spotted eagle nests resulted from their position on tree tops, at a height of 20–30 m and their quick drying out by sun and wind. It was also indicated by an enormously low number of species and individuals of mycetophagous beetles, which represent a significant component of the fauna in nests of other birds.

scholarly journals Draft Genome Sequence of Piscirickettsia litoralis , Isolated from Seawater

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Xuehua Wan ◽  
Alex J. Lee ◽  
Shaobin Hou ◽  
Blake Ushijima ◽  
Yen P. Nguyen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Salmonid Fish ◽  
Draft Genome Sequence ◽  
Free Living ◽  
Living Species

One species of Piscirickettsia , a pathogen of salmonid fish, has been described. The genome sequence of a putative second and free-living species may provide insights into the evolution of pathogenicity in the genus.

scholarly journals SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes

2021 ◽  
Vol 118 (52) ◽  
pp. e2116668118
Author(s):  
Paulina Pawlica ◽  
Therese A. Yario ◽  
Sylvia White ◽  
Jianhui Wang ◽  
Walter N. Moss ◽  
...  
Keyword(s):  
Small Rna ◽  
Leucine Zipper ◽  
Health Concern ◽  
Interferon Signaling ◽  
Basic Leucine Zipper ◽  
Argonaute Proteins ◽  
Evolutionarily Conserved ◽  
Core Components ◽  
Cellular Machinery ◽  
The Impact

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19), continues to be a pressing health concern. In this study, we investigated the impact of SARS-CoV-2 infection on host microRNA (miRNA) populations in three human lung-derived cell lines, as well as in nasopharyngeal swabs from SARS-CoV-2–infected individuals. We did not detect any major and consistent differences in host miRNA levels after SARS-CoV-2 infection. However, we unexpectedly discovered a viral miRNA-like small RNA, named CoV2-miR-O7a (for SARS-CoV-2 miRNA-like ORF7a-derived small RNA). Its abundance ranges from low to moderate as compared to host miRNAs and it associates with Argonaute proteins—core components of the RNA interference pathway. We identify putative targets for CoV2-miR-O7a, including Basic Leucine Zipper ATF-Like Transcription Factor 2 (BATF2), which participates in interferon signaling. We demonstrate that CoV2-miR-O7a production relies on cellular machinery, yet is independent of Drosha protein, and is enhanced by the presence of a strong and evolutionarily conserved hairpin formed within the ORF7a sequence.

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