Uncultured protist
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA369134 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5217061_1.fastq.gz | Fastqsanger.gz | |||
| SRR5217061_2.fastq.gz | Fastqsanger.gz | |||
| SRR5217151_1.fastq.gz | Fastqsanger.gz | |||
| SRR5217151_2.fastq.gz | Fastqsanger.gz | |||
| SRR5217173_1.fastq.gz | Fastqsanger.gz |
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Project description:Protists targeted sequencing of 18S rRNA HV 9
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Project description:Cleavage and polyadenylation are the final steps of eukaryotic mRNA 3' end formation. The most critical element in humans and other model organisms is the poly(A) signal, an AAUAAA hexamer. We recently discovered that the deeply branching eukaryote – Giardia lamblia uses a different but well-defined poly(A) signal, AGURAA. To better characterize when this evolutionary shift in the poly(A) signal occurred, we performed direct RNA sequencing of four protists within the Metamonada supergroup and two outgroup protists. Both outgroup protists and the non-Giardia Metamonada species use the AAUAAA poly(A) signal, indicating it is the ancestral signal. In contrast, all Giardia species use the WGURAA poly(A) signal, indicating it is a derived feature within Giardia or Fornicata. The change in this ubiquitous regulatory element raises questions about the sequence features that specify genuine poly(A) sites and how to avoid premature cleavage in the coding sequence. Therefore, we used a sequence classifier, a gapped k-mer support vector machine, that could discriminate between WGURAA sites in 3'UTRs and those in the CDS (F1 = 0.97). We found that Giardia lamblia uses nucleotides directly flanking the poly(A) signal for its recognition, with downstream nucleotides being the most important. Another member of the Giardia genus, Giardia muris, uses a different strategy: almost complete depletion of WGURAA hexamers in coding sequences. Ones that remain in the coding sequence can be recognized as poly(A) signals and undergo premature cleavage. These results identify unique features of the Giardia pathogens that could be targeted for drugs and highlight the diversity and evolution of mRNA 3' end formation in eukaryotes.
2024-08-01 | GSE260731 | GEO
Project description:global salterns eukaryotic V4 Metagenome
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Project description:In eukaryotes, pyruvate, a key metabolite produced by glycolysis, is converted by a mitochondrial pyruvate dehydrogenase complex (PDH) to acetyl-coenzyme A, which is fed into the tricarboxylic acid cycle. Two additional enzyme complexes catalyze similar oxidative decarboxylation reactions albeit using different substrates, the branched-chain ketoacid dehydrogenase (BCKDH) and the 2-oxoglutarate dehydrogenase (OGDH). In diplonemids, one of the most abundant and diverse groups of oceanic protists, comparative transcriptome analyses indicated that their PDH complex is compositionally unique, with the conventional E1 subunit replaced by an aceE protein of prokaryotic origin. Here we demonstrate in the model diplonemid Paradiplonema papillatum that the pyruvate dehydrogenase activity is comparable to that in other euglenozoan protists. By protein mass spectrometry we revealed that the aceE protein is twice as abundant as the E1 subunits of OGDH and enriched in the mitochondrion to the same level as the BCKDH E1 subunits, corroborating the functional relevance of the proposed aceE subunit of the PDH complex. Importantly, the acquisition of the archaeal aceE by the diplonemid ancestor led not only to the complete loss of the eukaryotic-type E1 of the PDH complex, but also its dedicated E2 and E3 subunits, still present in other euglenozoans. Hence, to reconstitute the diplonemid PDH, the aceE protein needs to partner with E2 and E3 subunits of BCKDH and/or OGDH. The diplonemid example illustrates that the acquisition and successful integration of a foreign E1p can profoundly reorganize the entire PDH complex.
2023-07-28 | PXD035104 | Pride
Project description:Termites harbor a symbiotic gut microbial community that is responsible for their ability to thrive on recalcitrant plant matter. The community comprises diverse microorganisms, most of which are as yet uncultivable; the detailed symbiotic mechanism remains unclear. Here, we present the first complete genome sequence of a termite gut symbiont-an uncultured bacterium named Rs-D17 belonging to the candidate phylum Termite Group 1 (TG1). TG1 is a dominant group in termite guts, found as intracellular symbionts of various cellulolytic protists, without any physiological information. To acquire the complete genome sequence, we collected Rs-D17 cells from only a single host protist cell to minimize their genomic variation and performed isothermal whole-genome amplification. This strategy enabled us to reconstruct a circular chromosome (1,125,857 bp) encoding 761 putative protein-coding genes. The genome additionally contains 121 pseudogenes assigned to categories, such as cell wall biosynthesis, regulators, transporters, and defense mechanisms. Despite its apparent reductive evolution, the ability to synthesize 15 amino acids and various cofactors is retained, some of these genes having been duplicated. Considering that diverse termite-gut protists harbor TG1 bacteria, we suggest that this bacterial group plays a key role in the gut symbiotic system by stably supplying essential nitrogenous compounds deficient in lignocelluloses to their host protists and the termites. Our results provide a breakthrough to clarify the functions of and the interactions among the individual members of this multilayered symbiotic complex.
| S-EPMC2291132 | biostudies-literature
Project description:BackgroundOur knowledge of the phylogeny and diversity of aquatic protists is rapidly increasing due to molecular surveys and next-generation sequencing approaches. This has led to a considerable discrepancy between the taxa known from cultures and those known from environmental 18S rRNA gene sequences. Hence, it is generally difficult to assign ecological functions to new taxa detected by culture-independent molecular approaches.Methodology/principal findingsA combination of unamended dark incubations and 18S rRNA sequencing was chosen to link molecular diversity data of uncultured protists with heterotrophic, presumably bacterivorous, growth. The incubations, conducted with Baltic Sea brackish water, resulted in a consistent shift from a protistan community dominated by phototrophs to one in which heterotrophs predominated. This was determined on the basis of cell abundance and 18S rRNA sequences derived from fingerprint analysis and clone libraries. The bulk of enriched phylotypes after incubation were related to hitherto uncultured marine taxa within chrysophytes, ochrophytes, choanoflagellates, cercozoans, and picobiliphytes, mostly represented in recently established or here defined environmental clades. Their growth in the dark, together with coinciding results from studies with a similar objective, provides evidence that these uncultured taxa represent heterotrophic or mixotrophic species.Conclusions/significanceThese findings shed some light into the trophic role of diverse uncultured protists especially within functionally heterogeneous groups (e.g., chrysophytes, ochrophytes) and groups that appear to be puzzling with regard to their nutrition (picobiliphytes). Additionally, our results indicate that the heterotrophic flagellate community in the southwestern Baltic Sea is dominated by species of marine origin. The combination of unamended incubations with molecular diversity analysis is thus confirmed as a promising approach to explore the trophic mode of environmentally relevant protist taxa for which only sequence data are currently available.
| S-EPMC3408427 | biostudies-literature