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 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:The molecular machine that synthesizes RNA in Eucarya and Archaea, RNA polymerase, is composed of 11 or 12 subunits M-^V 9 or 10 that form the core holoenzyme, and a heterodimer formed from subunits E and F that associates with the core.<br><br>In this study we used a recombinant archaeal MbRpoE/F heterodimer to capture cellular mRNA and a custom Agilent microarray to determine which mRNA it binds. Transcripts bound by the heterodimer were identified through competitive hybridization of the total RNA obtained from Methanococcoides burtonii and the RNA obtained through the selection of the transcripts that interact with the MbRpoE/F heterodimer bound to the column.
2011-03-01 | E-MEXP-2625 | biostudies-arrayexpress
Project description:Structural maintenance of chromosomes (SMC) complexes fold genomes by extruding DNA loops. In eukaryotes, loop-extruding SMC complexes form topologically associating domains (TADs) by being stalled by roadblock proteins. It remains unclear whether a similar mechanism of domain formation exists in prokaryotes. Using high-resolution chromosome conformation capture sequencing, we show that an archaeal homolog of the bacterial Smc-ScpAB complex organizes the genome of Thermococcus kodakarensis into TAD-like domains. We also find that TrmBL2, a nucleoid-associated protein that forms a stiff nucleoprotein filament, stalls the T. kodakarensis SMC complex and establishes a boundary at the site-specific recombination site dif. TrmBL2 stalls the SMC complex at tens of additional non-boundary loci with lower efficiency. Intriguingly, the stalling efficiency is correlated with shape properties of underlying DNA sequences. Our study illuminates not only a eukaryotic-like mechanism of domain formation in archaea, but also an unforeseen role of intrinsic DNA shape in large-scale genome organization.
2024-12-15 | GSE267298 | GEO
Project description:Since their discovery, archaea have not only proven a fascinating domain in their own right, but also helped us understand the evolution and function of molecular components they share with bacteria or eukaryotes. Archaeal histones are homologous to their eukaryotic counterparts, but operate in a less constrained bacterial-like cellular environment and their role in transcription and genome function remains obscure. In order to understand how archaeal histones affect transcriptional processes, we induced expression of the two histones from the archaeon Methanothermus fervidus in a naive bacterial system (E. coli) that has not evolved to integrate this kind of proteins. We show, using a series of MNase digestion experiments, that these histones bind the bacterial genome and wrap DNA in vivo in a pattern consistent with a previously proposed multimerisation model, in a similar pattern observed natively. We correlate genome-wide occupancy maps and gene expression profiles in different phases of growth to show that – although expression of archaeal histones triggers morphological changes in E. coli – there appears to only be an indirect effect on transcription. Since their discovery, archaea have not only proven a fascinating domain in their own right, but also helped us understand the evolution and function of molecular components they share with bacteria or eukaryotes. Archaeal histones are homologous to their eukaryotic counterparts, but operate in a less constrained bacterial-like cellular environment and their role in transcription and genome function remains obscure. In order to understand how archaeal histones affect transcriptional processes, we induced expression of the two histones from the archaeon Methanothermus fervidus in a naive bacterial system (E. coli) that has not evolved to integrate this kind of proteins. We show, using a series of MNase digestion experiments, that these histones bind the bacterial genome and wrap DNA in vivo in a pattern consistent with a previously proposed multimerisation model, in a similar pattern observed natively. We correlate genome-wide occupancy maps and gene expression profiles in different phases of growth to show that – although expression of archaeal histones triggers morphological changes in E. coli – there appears to only be an indirect effect on transcription.
2019-03-11 | GSE127678 | GEO