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From alpaca to zebrafish: hammerhead ribozymes wherever you look.

Seehafer, C. and Kalweit, A. and Steger, G. and Gräf, S. and Hammann, Christian (2011):
From alpaca to zebrafish: hammerhead ribozymes wherever you look.
In: RNA (New York, N.Y.), pp. 21-6, 17, (1), ISSN 1469-9001, [Article]

Abstract

The hammerhead ribozyme was originally discovered in subviral plant pathogens and was subsequently also found in a few other genomic locations. Using a secondary structure-based descriptor, we have searched publicly accessible sequence databases for new examples of type III hammerhead ribozymes. The more than 60,000 entries fulfilling the descriptor were filtered with respect to folding and stability parameters that were experimentally validated. This resulted in a set of 284 unique motifs, of which 124 represent database entries of known hammerhead ribozymes from subviral plant pathogens and A. thaliana. The remainder are 160 novel ribozyme candidates in 50 different eukaryotic genomes. With a few exceptions, the ribozymes were found either in repetitive DNA sequences or in introns of protein coding genes. Our data, which is complementary to a study by De la Peña and García-Robles in 2010, indicate that the hammerhead is the most abundant small endonucleolytic ribozyme, which, in view of no sequence conservation beyond the essential nucleotides, likely has evolved independently in different organisms.

Item Type: Article
Erschienen: 2011
Creators: Seehafer, C. and Kalweit, A. and Steger, G. and Gräf, S. and Hammann, Christian
Title: From alpaca to zebrafish: hammerhead ribozymes wherever you look.
Language: English
Abstract:

The hammerhead ribozyme was originally discovered in subviral plant pathogens and was subsequently also found in a few other genomic locations. Using a secondary structure-based descriptor, we have searched publicly accessible sequence databases for new examples of type III hammerhead ribozymes. The more than 60,000 entries fulfilling the descriptor were filtered with respect to folding and stability parameters that were experimentally validated. This resulted in a set of 284 unique motifs, of which 124 represent database entries of known hammerhead ribozymes from subviral plant pathogens and A. thaliana. The remainder are 160 novel ribozyme candidates in 50 different eukaryotic genomes. With a few exceptions, the ribozymes were found either in repetitive DNA sequences or in introns of protein coding genes. Our data, which is complementary to a study by De la Peña and García-Robles in 2010, indicate that the hammerhead is the most abundant small endonucleolytic ribozyme, which, in view of no sequence conservation beyond the essential nucleotides, likely has evolved independently in different organisms.

Journal or Publication Title: RNA (New York, N.Y.)
Volume: 17
Number: 1
Divisions: 10 Department of Biology > Ribogenetics
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10 Department of Biology
Date Deposited: 24 Jan 2011 10:15
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