Browse
Submit Data
Databases
API
Help

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Phylogenetic analysis of Group I marine archaeal rRNA sequences emphasizes the hidden diversity within the primary group Archaea.

ABSTRACT: Archaea form one of the three primary groups of extant life and are commonly associated with the extreme environments which many of their members inhabit. Currently, the Archaea are classified into two kingdoms, Crenarchaeota and Euryarchaeota, based on phylogenetic analysis of ribosomal RNA (rRNA) sequences. Molecular techniques allowing the retrieval and analysis of rRNA sequences from diverse environments are increasing our knowledge of archaeal diversity. This report describes the presence of marine Archaea in north-east Atlantic waters. Quantitative estimates indicated that the marine Archaea constitute 8 per cent of the total prokaryotic rRNA in Irish coastal waters. Phylogenetic analysis of the archaeal rRNA gene sequences revealed sufficient genetic diversity within Archaea to indicate that the current two-kingdom classification of Crenarchaeota and Euryarchaeota is restrictive.

SUBMITTER: McInerney JO

PROVIDER: S-EPMC1688723 | biostudies-other | 1997 Nov

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder.

Project description: Not available

| S-EPMC167425 | biostudies-other

Prevalence of transcription promoters within archaeal operons and coding sequences

Project description:This SuperSeries is composed of the following subset Series: GSE12923: Halobacterium salinarum NRC-1 growth curve, tiling arrays. GSE12977: Halobacterium salinarum NRC-1 growth curve GSE13108: Halobacterium salinarum NRC-1 conditional ChIP-chip for transcription initiation factor IIB 4 (TFBd) GSE7045: ChIP-Chip of General Transcription factors in Halobacterium NRC-1 GSE15786: Halobacterium sp. NRC-1 ChIP-chip for TFBa, TFBd and TFBf, high resolution array GSE15788: Halobacterium salinarum NRC-1 total RNA hybridization of TFBd overexpression versus Reference sample Despite knowledge of complex prokaryotic transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have played a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of ~64% of all genes including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein-DNA interaction datasets revealed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 3' ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes - events usually considered spurious or non-functional. With experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements Refer to individual Series

2010-05-17 | E-GEOD-13150 | biostudies-arrayexpress

Phylogenetic diversity of archaea and the archaeal ammonia monooxygenase gene in uranium mining-impacted locations in Bulgaria.

Project description: Not available

| S-EPMC3966351 | biostudies-literature

Prevalence of transcription promoters within archaeal operons and coding sequences

Project description:Despite knowledge of complex prokaryotic transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have played a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of ~64% of all genes including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein-DNA interaction datasets revealed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 3' ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes - events usually considered spurious or non-functional. With experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements This SuperSeries is composed of the SubSeries listed below.

2009-06-25 | GSE13150 | GEO

Targeted diversity generation by intraterrestrial archaea and archaeal viruses.

Project description: Not available

| S-EPMC4372165 | biostudies-literature

A phylogenetic tree of 16S rRNA sequences from sulfate-reducing bacteria in a sandy marine sediment.

Project description: Not available

| S-EPMC201826 | biostudies-other

Phylogenetic diversity of sequences of cyanophage photosynthetic gene psbA in marine and freshwaters.

Project description: Not available

| S-EPMC2546643 | biostudies-literature

Protists Within Corals: The Hidden Diversity.

Project description: Not available