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Irina R Arkhipova – 1st expert on this subject based on the ideXlab platform
multitasking of the pirna silencing machinery targeting transposable elements and foreign genes in the Bdelloid Rotifer adineta vagaGenetics, 2016Co-Authors: Fernando Rodriguez, Irina R ArkhipovaAbstract:
RNA-mediated silencing processes play a key role in silencing of transposable elements, especially in the germ line, where piRNAs are responsible for suppressing transposon mobility and maintaining genome integrity. We previously reported that the genome of Adineta vaga , the first sequenced representative of the phylum Rotifera (class Bdelloidea), is characterized by massive levels of horizontal gene transfer, by unusually low transposon content, and by highly diversified RNA-mediated silencing machinery. Here, we investigate genome-wide distribution of pi-like small RNAs, which in A. vaga are 25-31 nucleotides in length and have a strong 5′ uridine bias, while lacking ping-pong amplification signatures. In agreement with expectations, 71% of mapped reads corresponded to annotated transposons, with 93% of these reads being in the antisense orientation. Unexpectedly, a significant fraction of piRNAs originates from predicted coding regions corresponding to genes of putatively foreign origin. The distribution of piRNAs across foreign genes is not biased towards 3′-UTRs, instead resembling transposons in uniform distribution pattern throughout the gene body, and in predominantly antisense orientation. We also find that genes with small RNA coverage, including a number of genes of metazoan origin, are characterized by higher occurrence of telomeric repeats in the surrounding genomic regions, and by higher density of transposons in the vicinity, which have the potential to promote antisense transcription. Our findings highlight the complex interplay between RNA-based silencing processes and acquisition of genes at the genome periphery, which can result either in their loss or eventual domestication and integration into the host genome.
endonuclease containing penelope retrotransposons in the Bdelloid Rotifer adineta vaga exhibit unusual structural features and play a role in expansion of host gene familiesMobile Dna, 2013Co-Authors: Irina R Arkhipova, Irina A Yushenova, Fernando RodriguezAbstract:
Penelope-like elements (PLEs) are an enigmatic group of retroelements sharing a common ancestor with telomerase reverse transcriptases. In our previous studies, we identified endonuclease-deficient PLEs that are associated with telomeres in Bdelloid Rotifers, small freshwater invertebrates best known for their long-term asexuality and high foreign DNA content. Completion of the high-quality draft genome sequence of the Bdelloid Rotifer Adineta vaga provides us with the opportunity to examine its genomic transposable element (TE) content, as well as TE impact on genome function and evolution.
genomic evidence for ameiotic evolution in the Bdelloid Rotifer adineta vagaNature, 2013Co-Authors: Jean-françois Flot, Boris Hespeels, Xiang Li, Irina R Arkhipova, Benjamin Noel, Etienne G J Danchin, Andreas Hejnol, Bernard HenrissatAbstract:
The genome of the asexual Rotifer Adineta vaga lacks homologous chromosomes; instead, its allelic regions are rearranged and sometimes found on the same chromosome in a palindromic fashion, a structure reminiscent of the primate Y chromosome and of other mitotic lineages such as cancer cells.
Claudia Ricci – 2nd expert on this subject based on the ideXlab platform
surviving starvation changes accompanying starvation tolerance in a Bdelloid RotiferJournal of Morphology, 2012Co-Authors: Roberto Marotta, Claudia Ricci, Andrea Uggetti, Francesca Leasi, Giulio MeloneAbstract:
Bdelloid Rotifers survive desiccation and starvation by halting activity and entering a kind of dormancy. To understand the mechanisms of survival in the absence of food source, we studied the anatomical and ultrastructural changes occurring in a Bdelloid species, Macrotrachela quadricornifera Milne 1886, after starvation for different periods. The starved Rotifers present a progressive reduction of body size accompanied with a consistent reduction of the volume of the stomach syncytium, where lipid inclusions and digestive vacuoles tend to fade with prolonged starvation. Similar reduction occurs in the vitellarium gland, in which yolk granules progressively decrease in number and size. The changes observed in the syncytia of the stomach and the vitellarium suggest that during starvation M. quadricornifera uses resources diverted from the stomach syncytium first and from the vitellarium syncytium later, resources that are normally allocated to reproduction. The fine structure of starved Bdelloids is compared with that of anhydrobiotic Bdelloids, revealing that survival during either forms of dormancy is sustained by different physiological mechanisms. J. Morphol., 2011. © 2011 Wiley Periodicals, Inc.
dry and survive morphological changes during anhydrobiosis in a Bdelloid RotiferJournal of Structural Biology, 2010Co-Authors: Roberto Marotta, Claudia Ricci, Andrea Uggetti, Francesca Leasi, Giulio MeloneAbstract:
Abstract Bdelloid Rotifers are aquatic microinvertebrates able to cope with the loss of environmental water by entering dormancy, and are thus capable of living in temporary habitats. When water is evaporating, Bdelloids contract into “tuns”, silence metabolism and lose water from the body, a condition known as anhydrobiosis. Under controlled conditions, a Bdelloid species ( Macrotrachela quadricornifera ) was made anhydrobiotic, and its morphology was studied by light, confocal and electron microscopy. A compact anatomy characterizes the anhydrobiotic Rotifer, resulting in a considerable reduction of its body volume: the internal organs, precisely packed together, occupy the body cavity almost completely and the lumen of hollow organs disappears. Remarkable ultrastructural changes characterize the anhydrobiotic condition. The mitochondria are wholly surrounded by a ring of electron-dense particles, and the epidermal pores, open in the hydrated specimens, become gradually closed by structures similar to epithelial junctions. The cilia are densely packed: microtubules are still identifiable, but the axonemal organization appears disrupted. This is the first extensive comparative study on the morphological changes associated with the anhydrobiosis process in a Rotifer, providing the basis for an improved understanding of the processes involved in this extreme adaptation.
first description of the serotonergic nervous system in a Bdelloid Rotifer macrotrachela quadricornifera milne 1886 philodinidaeZoologischer Anzeiger – A Journal of Comparative Zoology, 2009Co-Authors: Francesca Leasi, Roberta Pennati, Claudia RicciAbstract:
Abstract Class Bdelloidea of phylum Rotifera comprises aquatic microinvertebrates that are known for both obligate parthenogenesis and for resisting desiccation through a dormant reversible state. In the frame of an investigation about the role of the nervous system in controlling life cycle, reproduction and dormancy, we describe the serotonergic system of a Bdelloid, Macrotrachela quadricornifera , using serotonin immunohistochemistry and confocal laser scanning microscopy. Serotonin immunoreactivity is present in the cerebral ganglion, lateral nerve cords and peripheral neurites. The cerebral ganglion consists of perikarya that send neurites cephalically to the rostrum and corona. A pair of neurites exits the cerebral ganglion as lateral nerve cords, and proceeds caudally to the pedal ganglion where additional neurites enter the foot. Based on the location of serotonergic immunoreactivity, we hypothesize that the neurotransmitter is involved in both motor activity (e.g., ciliary beating, inchworm-like locomotion) and sensory activity. A comparison between the serotonergic nervous systems of M. quadricornifera and species of Monogononta reveals differences in the numbers and patterns of cerebral perikarya, peripheral perikarya, and periperhal neurites. These differences may have functional significance for understanding adaptations to specific environments and/or systematic significance for reconstructing the Rotiferan ground pattern.
Alan Tunnacliffe – 3rd expert on this subject based on the ideXlab platform
multiple horizontally acquired genes from fungal and prokaryotic donors encode cellulolytic enzymes in the Bdelloid Rotifer adineta ricciaeGene, 2015Co-Authors: L Szydlowski, Chiara Boschetti, Alastair Crisp, E G G Barbosa, Alan TunnacliffeAbstract:
Abstract The Bdelloid Rotifer, Adineta ricciae, an anhydrobiotic microinvertebrate, exhibits a high rate of horizontal gene transfer (HGT), with as much as 10% of its transcriptome being of foreign origin. Approximately 80% of these foreign transcripts are involved in metabolic processes, and therefore Bdelloids represent a useful model for assessing the contribution of HGT to biochemical diversity. To validate this concept, we focused on cellulose digestion, an unusual activity in animals, which is represented by at least 16 genes encoding cellulolytic enzymes in A. ricciae. These genes have been acquired from a variety of different donor organisms among the bacteria and fungi, demonstrating that Bdelloids use diverse genetic resources to construct a novel biochemical pathway. A variable complement of the cellulolytic gene set was found in five other Bdelloid species, indicating a dynamic process of gene acquisition, duplication and loss during Bdelloid evolution. For example, in A. ricciae, gene duplications have led to the formation of three copies of a gene encoding a GH45 family glycoside hydrolase, at least one of which encodes a functional enzyme; all three of these gene copies are present in a close relative, Adineta vaga, but only one copy was found in each of four Rotaria species. Furthermore, analysis of expression levels of the cellulolytic genes suggests that a bacterial-origin cellobiase is upregulated upon desiccation. In summary, Bdelloid Rotifers have apparently developed cellulolytic functions by the acquisition and domestication of multiple foreign genes.
trafficking of Bdelloid Rotifer late embryogenesis abundant proteinsThe Journal of Experimental Biology, 2012Co-Authors: Rashmi Tripathi, Chiara Boschetti, Brian Mcgee, Alan TunnacliffeAbstract:
SUMMARY The Bdelloid Rotifer Adineta ricciae is an asexual microinvertebrate that can survive desiccation by entering an ametabolic state known as anhydrobiosis. Two late embryogenesis abundant (LEA) proteins, ArLEA1A and ArLEA1B, have been hypothesized to contribute to desiccation tolerance in these organisms, since in vitro assays suggest that ArLEA1A and ArLEA1B stabilize desiccation-sensitive proteins and membranes, respectively. To examine their functions in vivo , it is important to analyse the cellular distribution of the Bdelloid LEA proteins. Bioinformatics predicted their translocation into the endoplasmic reticulum (ER) via an N-terminal ER translocation signal and persistence in the same compartment via a variant C-terminal retention signal sequence ATEL. We assessed the localization of LEA proteins in Bdelloids and in a mammalian cell model. The function of the N-terminal sequence of ArLEA1A and ArLEA1B in mediating ER translocation was verified, but our data showed that, unlike classical ER-retention signals, ATEL allows progression from the ER to the Golgi and limited secretion of the proteins into the extracellular medium. These results suggest that the N-terminal ER translocation signal and C-terminal ATEL sequence act together to regulate the distribution of Rotifer LEA proteins within intracellular vesicular compartments, as well as the extracellular space. We speculate that this mechanism allows a small number of LEA proteins to offer protection to a large number of desiccation-sensitive molecules and structures both inside and outside cells in the Bdelloid Rotifer.
foreign genes and novel hydrophilic protein genes participate in the desiccation response of the Bdelloid Rotifer adineta ricciaeThe Journal of Experimental Biology, 2011Co-Authors: Chiara Boschetti, Natalia N Pouchkinastantcheva, Pia Hoffmann, Alan TunnacliffeAbstract:
Bdelloid Rotifers are aquatic micro-invertebrates with the ability to survive extreme desiccation, or anhydrobiosis, at any life stage. To gain insight into the molecular mechanisms used by Bdelloids during anhydrobiosis, we constructed a cDNA library enriched for genes that are upregulated in Adineta ricciae 24 h after onset of dehydration. Resulting expressed sequence tags (ESTs) were analysed and sequences grouped into categories according to their probable identity. Of 75 unique sequences, approximately half (36) were similar to known genes from other species. These included genes encoding an unusual group 3 late embryogenesis abundant protein, and a number of other stress-related and DNA repair proteins. Open reading frames from a further 39 novel sequences, without counterparts in the database, were screened for the characteristics of intrinsically disordered proteins, i.e. hydrophilicity and lack of stable secondary structure. Such proteins have been implicated in desiccation tolerance and at least five were found. The majority of the genes identified was confirmed by real-time quantitative PCR to be capable of upregulation in response to evaporative water loss. Remarkably, further database and phylogenetic analysis highlighted four ESTs that are present in the A. ricciae genome but which represent genes probably arising from fungi or bacteria by horizontal gene transfer. Therefore, not only can Bdelloid Rotifers accumulate foreign genes and render them transcriptionally competent, but their expression pattern can be modified for participation in the desiccation stress response, and is presumably adaptive in this context.
: Basic Local Alignment Search Tool
: expressed sequence tag
: grand average hydropathy
: horizontal gene transfer
: intrinsically disordered protein
: late embryogenesis abundant
: open reading frame
: polymerase chain reaction
: predictor of natural disordered regions
: relative humidity
: reactive oxygen species