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Revealing gene transcription and translation initiation patterns in archaea, using an interactive clustering model

Authors :
Xiu-Feng Wan
Susan M. Bridges
John A. Boyle
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.

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