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Revealing gene transcription and translation initiation patterns in archaea, using an interactive clustering model
- Source :
- Extremophiles. 8:291-299
- Publication Year :
- 2004
- Publisher :
- Springer Science and Business Media LLC, 2004.
-
Abstract
- An interactive clustering model based on positional weight matrices is described and results obtained using the model to analyze gene regulation patterns in archaea are presented. The 5' flanking sequences of ORFs identified in four archaea, Sulfolobus solfataricus, Pyrobaculum aerophilum, Halobacterium sp. NRC-1, and Pyrococcus abyssi, were clustered using the model. Three regular patterns of clusters were identified for most ORFs. One showed genes with only a ribosome-binding site; another showed genes with a transcriptional regulatory region located at a constant location with respect to the start codon. A third pattern combined the previous two. Both P. aerophilum and Halobacterium sp. NRC-1 exhibited clusters of genes that lacked any regular pattern. Halobacterium sp. NRC-1 also presented regular features not seen in the other organisms. This group of archaea seems to use a combination of eubacterial and eukaryotic regulatory features as well as some unique to individual species. Our results suggest that interactive clustering may be used to examine the divergence of the gene regulatory machinery in archaea and to identify the presence of archaea-specific gene regulation patterns.
- Subjects :
- Halobacterium
Transcription, Genetic
ved/biology.organism_classification_rank.species
Microbiology
Genes, Archaeal
Sulfolobus
Open Reading Frames
Eukaryotic translation
Pyrococcus
ORFS
Genetics
biology
ved/biology
Sulfolobus solfataricus
General Medicine
biology.organism_classification
Archaea
Genetic translation
Open reading frame
Multigene Family
Protein Biosynthesis
Molecular Medicine
Gene Expression Regulation, Archaeal
Databases, Nucleic Acid
Ribosomes
Pyrococcus abyssi
Subjects
Details
- ISSN :
- 14334909 and 14310651
- Volume :
- 8
- Database :
- OpenAIRE
- Journal :
- Extremophiles
- Accession number :
- edsair.doi.dedup.....7f270b8336507cfb57ff7b7ec180d5a2
- Full Text :
- https://doi.org/10.1007/s00792-004-0388-1