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An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes
1Department of Biochemistry, University of Nebraska, Lincoln, NE 68588-0664, USA.
Bioinformatics (Oxford, England)
|March 31, 2005
Summary
Researchers identified a conserved guanosine in bacterial SECIS elements, crucial for selenocysteine incorporation. This led to a new tool, bSECISearch, for finding selenoprotein genes and understanding bacterial selenoproteomes.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Selenocysteine (Sec) incorporation into proteins uses UGA codons and a cis-acting RNA structure, the Sec insertion sequence (SECIS) element.
- While bacterial SECIS elements in E. coli are known, a general bacterial SECIS consensus structure is missing.
Purpose of the Study:
- To develop a bacterial SECIS consensus model.
- To create a computational tool for identifying bacterial SECIS elements and selenoprotein genes.
Main Methods:
- Developed a bacterial SECIS consensus model based on structural features.
- Built the bSECISearch computational tool for sequence database analysis.
Main Results:
- Identified a conserved guanosine in the apical loop as a key feature of the bacterial SECIS consensus.
- bSECISearch detected 96.5% of known selenoprotein genes in bacterial genomes and predicted new ones.
- Bacterial selenoproteomes range from 1 to 11 selenoproteins, with formate dehydrogenase being common.
Conclusions:
- The bacterial SECIS consensus model and bSECISearch tool aid in accurate selenoprotein gene annotation.
- Facilitates the characterization of diverse bacterial selenoproteomes.