Archaeal survey
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB13734 | ENA |
REPOSITORIES: ENA
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Project description:Organisms of the third domain of life, the Archaea, share molecular characteristics both with bacteria and eukarya. These organisms attract scientific attention as research models for regulation and evolution of processes such as transcription, translation and RNA processing. We have reconstructed the primary transcriptome of Sulfolobus solfataricus P2, one of the most widely studied model archaeal organisms. Analysis of 625 million bases of sequenced cDNAs yielded a single-bp resolution map of transcription start sites and operon structures for more than 1000 transcriptional units. The analysis led to the discovery of 310 expressed non-coding RNAs, with an extensive expression of overlapping cis-antisense transcripts to a level unprecedented in any bacteria or archaea but resembling that of eukaryotes. As opposed to bacterial transcripts, most Sulfolobus transcripts completely lack 5' UTR sequences, suggesting that mRNA/ncRNA interactions differ between bacteria and archaea. The data also reveal internal hotspots for transcript cleavage linked to RNA degradation, and predict sequence motifs that promote RNA destabilization. This study emphasizes the importance of transcriptome sequencing as a key tool for understanding the mechanisms and extent of RNA-based regulation for bacteria and archaea. 5 samples of cDNA sequencing (2 of these are replicates), and 3 samples of RACE-cDNA sequencing (described in the samples section).
2009-10-21 | E-GEOD-18630 | biostudies-arrayexpress
Project description:Organisms of the third domain of life, the Archaea, share molecular characteristics both with bacteria and eukarya. These organisms attract scientific attention as research models for regulation and evolution of processes such as transcription, translation and RNA processing. We have reconstructed the primary transcriptome of Sulfolobus solfataricus P2, one of the most widely studied model archaeal organisms. Analysis of 625 million bases of sequenced cDNAs yielded a single-bp resolution map of transcription start sites and operon structures for more than 1000 transcriptional units. The analysis led to the discovery of 310 expressed non-coding RNAs, with an extensive expression of overlapping cis-antisense transcripts to a level unprecedented in any bacteria or archaea but resembling that of eukaryotes. As opposed to bacterial transcripts, most Sulfolobus transcripts completely lack 5' UTR sequences, suggesting that mRNA/ncRNA interactions differ between bacteria and archaea. The data also reveal internal hotspots for transcript cleavage linked to RNA degradation, and predict sequence motifs that promote RNA destabilization. This study emphasizes the importance of transcriptome sequencing as a key tool for understanding the mechanisms and extent of RNA-based regulation for bacteria and archaea.
2009-10-21 | GSE18630 | GEO
Project description:We use MNase-Seq to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. Like all members of the Thermoplasmatales, T. acidophilum harbours a HU family protein, HTa, that is highly expressed and protects - like histones but unlike well-characterized bacterial HU proteins – a sizeable fraction of the genome from MNase digestion. Comparing HTa-based chromatin architecture to that of three histone-encoding archaea, Methanothermus fervidus, Haloferax volcanii, and Thermococcus kodakkarensis, we present evidence that HTa is an archaeal histone analog. HTa-protected fragments are GC-rich, display histone-like mono- and dinucleotide patterns around the dyad, exhibit relatively invariant positioning throughout the growth cycle, and show archaeal histone-like oligomerization dynamics. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.
2019-03-11 | GSE127727 | GEO
Project description:Histones are a principal constituent of chromatin in eukaryotes and fundamental to our understanding of eukaryotic gene regulation. In archaea, histones are phylogenetically widespread but not universal: several archaeal lineages have independently lost histone genes. What prompted or facilitated these losses and how archaea without histones organize their chromatin remains largely unknown. Here, we use micrococcal nuclease digestion of native and reconstituted chromatin to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. We confirm and extend prior results showing that T. acidophilum harbours a HU family protein, HTa, that protects part of the genome from MNase digestion. Charting HTa-based chromatin architecture in vitro, in vivo and in an HTa-expressing E. coli strain, we present evidence that HTa is an archaeal histone analog. HTa-protected fragments are GC-rich, display histone-like mono- and dinucleotide patterns around a conspicuous dyad, exhibit relatively invariant positioning throughout the growth cycle, and show archaeal histone-like oligomerization behaviour. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.
2019-10-08 | GSE138576 | GEO
Project description:We use MNase-Seq to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. Like all members of the Thermoplasmatales, T. acidophilum harbours a HU family protein, HTa, that is highly expressed and protects - like histones but unlike well-characterized bacterial HU proteins – a sizeable fraction of the genome from MNase digestion. Comparing HTa-based chromatin architecture to that of three histone-encoding archaea, Methanothermus fervidus, Haloferax volcanii, and Thermococcus kodakkarensis, we present evidence that HTa is an archaeal histone analog. HTa-protected fragments are GC-rich, display histone-like mono- and dinucleotide patterns around the dyad, exhibit relatively invariant positioning throughout the growth cycle, and show archaeal histone-like oligomerization dynamics. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.
2019-03-11 | GSE127726 | GEO
Project description:Chromosome conformation capture (3C) technologies have identified topologically associating domains (TADs) and larger A/B compartments as two salient structural features of eukaryotic chromosomes. These structures are sculpted by the combined actions of transcription and structural maintenance of chromosomes (SMC) superfamily proteins. Bacterial chromosomes fold into TAD-like chromosomal interaction domains (CIDs) but do not display A/B compartment-type organization. Here, we reveal that chromosomes of Sulfolobus archaea are organized into CID-like topological domains in addition to the larger A/B compartment-type structures that we described recently. We uncover local rules governing the identity of the topological domains. We also identify long-range loop structures which provide evidence of a hub-like structure that colocalizes genes involved in ribosome biogenesis. In addition to providing high resolution description of archaeal chromosome architectures, our data provide evidence for multiple modes of organization in prokaryotic chromosomes and yield novel insight into the evolution of eukaryotic chromosome conformation.
2020-12-28 | GSE159537 | GEO
Project description:The cell cycle is a precisely coordinated series of events of cell growth, DNA replication and cell division, all of which are imperative for the proliferation of organisms. Archaea of the order Sulfolobales exhibit a cell cycle similar to that of eukaryotes. It has been suggested that the proteasome degradation of the cell division protein CdvB controls the progression of cell division. This raises a question regarding the regulation of proteosome activity in these archaea. In this paper, we report that an ArsR family cyclically-transcribed cell cycle transcription factor, CCTF1 (cell cycle transcription factor 1), plays a decisive role in regulation of the proteasome activity. We revealed that transcription of the proteasome regulatory subunit PAN (proteasome-activating nucleotidase) is specifically regulated by CCTF1 through binding to an AT-rich palindromic sequence. We show that CCTF1, rather than aCcrK (ePK2), is the key factor controlling the proteasome activity. Our study provides important insights into the proteosome-mediated cell cycle regulation mechanism in archaea.
2026-08-01 | GSE333795 | GEO
Project description:The cell cycle is a precisely coordinated series of events of cell growth, DNA replication and cell division, all of which are imperative for the proliferation of organisms. Archaea of the order Sulfolobales exhibit a cell cycle similar to that of eukaryotes. It has been suggested that the proteasome degradation of the cell division protein CdvB controls the progression of cell division. This raises a question regarding the regulation of proteosome activity in these archaea. In this paper, we report that an ArsR family cyclically-transcribed cell cycle transcription factor, CCTF1 (cell cycle transcription factor 1), plays a decisive role in regulation of the proteasome activity. We revealed that transcription of the proteasome regulatory subunit PAN (proteasome-activating nucleotidase) is specifically regulated by CCTF1 through binding to an AT-rich palindromic sequence. We show that CCTF1, rather than aCcrK (ePK2), is the key factor controlling the proteasome activity. Our study provides important insights into the proteosome-mediated cell cycle regulation mechanism in archaea.
2026-08-01 | GSE333794 | GEO
Project description:The three-dimensional organization of chromosomes can have a profound impact on their replication and expression. The chromosomes of higher eukaryotes possess discrete compartments that are characterized by differing transcriptional activities. Contrastingly, most bacterial chromosomes have simpler organization with local domains, the boundaries of which are influenced by gene expression. Numerous studies have revealed that the higher-order architectures of bacterial and eukaryotic chromosomes are dependent on the actions of Structural Maintenance of Chromosomes (SMC) superfamily protein complexes, in particular the near-universal condensin complex. Intriguingly, however, many archaea, including members of the genus Sulfolobus do not encode canonical condensin. We describe chromosome conformation capture experiments on Sulfolobus species. These reveal the presence of distinct domains along Sulfolobus chromosomes that undergo discrete and specific higher-order interactions, thus defining two compartment types. We observe causal linkages between compartment identity, gene expression and binding of a hitherto uncharacterized SMC superfamily protein that we term “coalescin”.
2019-09-19 | GSE128063 | GEO
Project description:Peptidoglycan (PG) is a fundamental component of bacterial envelopes, and it is processed by a wide range of hydrolases during cell growth and division1–3. In contrast, in Archaea only one clade -regrouping the Methanobacteriales and the Methanopyrales- possess cell walls made of PG (arcPG)4–6. The structure of arcPG (also known as pseudomurein) was resolved in the 80s by purely chemical methods7–11. Despite its overall similarity to bacterial PG, arcPG has striking structural differences, notably it lacks N-Acetylmuramic acid (MurNAc) but instead has N-Acetyltalosaminuronic acid (TalNAc), and GlcNAc and TalNAc are connected via unique (1,3) glycosidic bonds6. These peculiarities make arcPG insensitive to muramidases active on bacterial PG such as lysozyme or mutanolysin. To date, no glycosyl hydrolase cleaving arcPG has been described. Here we report the discovery and characterization of TalA, the first enzyme with Talosaminidase activity from Methanobrevibacter smithii, the most abundant species of walled methanogenic archaea from the human gut. It is a dual function enzyme, cleaving both the peptide stem and glycan strand. The identification of TalA allowed us to revise the chemical structure of arcPG, revealing the presence of a previously undescribed modification on the Talosaminuronic acid moiety which appears to be a conserved feature in all walled archaea. Phylogenetic analysis and taxonomic distribution show that TalA homologues are specific to walled archaea, and we experimentally demonstrate that M. smithii TalA is active on arcPG from diverse archaea. Finally, quantitative and high-resolution imaging of TalA subcellular localization indicates it is the main hydrolase involved in septum cleavage in walled archaea, also confirmed by the phenotype of a TalA mutant. Our results identify a novel enzyme involved in the archaeal cell cycle and establish an essential tool to further study the biology of walled archaea both in vitro and in vivo. These findings also open important perspectives toward the development of mitigation strategies for methanogens in man-made and natural environments, including the gastrointestinal tract.
2026-05-19 | PXD052257 | Pride