Archaea
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR261008_1.fastq.gz | Fastqsanger.gz | |||
| DRR261008_2.fastq.gz | Fastqsanger.gz | |||
| DRR261009_1.fastq.gz | Fastqsanger.gz | |||
| DRR261009_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Chromosome segregation is a vital process for all organisms. The mechanisms underpinning chromosomal partitioning in the archaeal domain remain elusive. Our group has identified the first chromosome segregation system in thermophilic archaea. Sulfolobus solfataricus partition system consists of SegA, an orthologue of bacterial Walker-type ParA proteins; SegB, an archaea-specific DNA binding protein and a cis-acting DNA region. ChIP-seq experiments disclosed multiple SegB binding sites scattered over the chromosome and revealed a novel DNA binding motif.
2025-06-25 | GSE169604 | GEO
Project description:The social life of archaea is poorly understood. In particular, even though competition and conflict are common themes in microbial communities, there is scant evidence documenting antagonistic interactions between archaea and their abundant prokaryotic brethren: bacteria. Do archaea specifically target bacteria for destruction? If so, what molecular weaponry do they use? Here, we present an approach to infer antagonistic interactions between archaea and bacteria from genome sequence. We show that a large and diverse set of archaea encode peptidoglycan hydrolases, enzymes that recognize and cleave a structure – peptidoglycan – that is a ubiquitous component of bacterial cell walls but absent from archaea. We predict the bacterial targets of archaeal peptidoglycan hydrolases using a structural homology approach and demonstrate that the predicted target bacteria tend to inhabit a similar niche to the archaeal producer, indicative of ecologically relevant interactions. Using a heterologous expression system, we demonstrate that two peptidoglycan hydrolases from the halophilic archaeaon Halogranum salarium B-1 kill the halophilic bacterium Halalkalibacterium halodurans, a predicted target, and do so in a manner consistent with peptidoglycan hydrolase activity. Our results suggest that, even though the tools and rules of engagement remain largely unknown, archaeal-bacterial conflicts are likely common, and we present a roadmap for the discovery of additional antagonistic interactions between these two domains of life. Our work has implications for understanding mixed microbial communities that include archaea and suggests that archaea might represent a large untapped reservoir of novel antibacterials.
2026-02-07 | PXD064732 | Pride
Project description:Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Though recently discovered, trace gas oxidation is now recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. While trace gas oxidation has been reported in nine phyla of bacteria, it was not known whether archaea also use atmospheric H2. Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H2 and CO to sub-atmospheric levels. Oxidation occurred during both growth and survival across a wide range of temperatures (10 to 70°C). Genomic analysis demonstrated that A. brierleyi encodes a canonical carbon monoxide dehydrogenase and, unexpectedly, four distinct [NiFe]-hydrogenases from subgroups not known to mediate aerobic H2 uptake. Quantitative proteomic analyses showed that A. brierleyi differentially produced these enzymes in response to electron donor and acceptor availability. A previously unidentified group 1 [NiFe]-hydrogenase, with a unique genetic arrangement, is constitutively expressed and upregulated during stationary phase and aerobic hydrogenotrophic growth. Another archaeon, Metallosphaera sedula, was also found to oxidize atmospheric H2. These results suggest that trace gas oxidation is a common trait of aerobic archaea, which likely plays a role in their survival and niche expansion, including during dispersal through temperate environments. These findings also demonstrate that atmospheric H2 consumption is a cross-domain phenomenon, suggesting an ancient origin of this trait, and identify previously unknown microbial and enzymatic sinks of atmospheric H2 and CO.
2024-02-26 | PXD040286 | Pride
Project description:ammonia-oxidizing archaea Genome sequencing
| PRJNA609401 | ENA
Project description:Structure probing combined with next-generation sequencing (NGS) has provided novel insights into RNA structure-function relationships. To date such studies have focused largely on bacteria and eukaryotes, with little attention given to the third domain of life, archaea. Furthermore, functional RNAs have not been extensively studied in archaea, leaving open questions about RNA structure and function within this domain of life. With archaeal species being diverse and having many similarities to both bacteria and eukaryotes, the archaea domain has the potential to be an evolutionary bridge. In this study, we introduce a method for probing RNA structure in vivo in the archaea domain of life. We investigated the structure of ribosomal RNA (rRNA) from Methanosarcina acetivorans, a well-studied anaerobic archaeal species, grown with either methanol or acetate. After probing the RNA in vivo with dimethyl sulfate (DMS), Structure-seq2 libraries were generated, sequenced, and analyzed. We mapped the reactivity of DMS onto the secondary structure of the ribosome, which we determined independently with comparative analysis, and confirmed the accuracy of DMS probing in M. acetivorans. Accessibility of the rRNA to DMS in the two carbon sources was found to be quite similar, although some differences were found. Overall, this study establishes the Structure-seq2 pipeline in the archaea domain of life and informs about ribosomal structure within M. acetivorans.
2023-06-27 | GSE229536 | GEO
Project description:Chromosome segregation is a fundamental process in all life forms and requires coordination with genome organization, replication and cell division. The mechanism that mediates chromosome segregation in archaea remains enigmatic, despite the centre-stage role assumed by these organisms in the discourse about the origin of eukaryotes. Previously, we identified two proteins, SegA and SegB, which form a minimalist chromosome partition machine in Sulfolobales. Here we uncover patterns and mechanisms that the SegAB system employs to link chromosome organization to genome segregation. Deletion of the genes causes growth and chromosome partition defects. ChIP-seq investigations revealed that SegB binds to multiple sites scattered across the chromosome, but mainly localised close to the segAB locus in most of the examined archaeal genera. The sites are predominantly present in intragenic regions. Recent chromosome conformation studies have shown that the chromosome of Sulfolobales members is organised into two spatially segregated compartments, designated A and B. Interestingly, SegB sites are predominantly located in the A compartment, whose shaping factors have remained elusive so far. We show that SegB coalesces into multiple foci through the nucleoid, exhibiting a biased localisation towards the cell periphery, which hints at potential tethers to the cell membrane. This clue is further strengthened by the structural similarities of SegB orthologues with predicted b-helix domains to membrane-associate proteins, including the distant bactofilin. Atomic force microscopy experiments provided mechanistic insights into how SegB binds DNA and uncovered short-range DNA compaction and long-range looping of distant sites by SegB. These activities point to a significant role for SegB in chromosome condensation that in turn enables genome segregation. Collectively, our data put forward SegAB as important players in bridging chromosome organization to genome segregation in archaea.
2025-06-22 | GSE297822 | GEO