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

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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.

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Acknowledgements

We thank two anonymous reviewers for their critical suggestion for the revision of the initial manuscript.

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Author notes

  1. Xiu-Feng Wan

    Present address: Digital Biology Laboratory, University of Missouri Columbia, Columbia, MO 65211, USA

Authors and Affiliations

  1. Department of Computer Science and Engineering, Mississippi State University, Mississippi State, MS 39762, USA

    Xiu-Feng Wan & Susan M. Bridges

  2. Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, MS 39762, USA

    John A. Boyle

Authors
  1. Xiu-Feng Wan
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  2. Susan M. Bridges
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  3. John A. Boyle
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Correspondence to Susan M. Bridges.

Additional information

Communicated by K. Horikoshi and F. Robb

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Wan, XF., Bridges, S.M. & Boyle, J.A. Revealing gene transcription and translation initiation patterns in archaea, using an interactive clustering model. Extremophiles 8, 291–299 (2004). https://doi.org/10.1007/s00792-004-0388-1

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  • DOI: https://doi.org/10.1007/s00792-004-0388-1

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