Abstract
BackgroundPost transcriptional gene silencing (PTGS) is a recently discovered phenomenon that is an area of intense research interest. Components of the PTGS machinery are being discovered by genetic and bioinformatics approaches, but the picture is not yet complete.ResultsThe gene for the PTGS impaired Arabidopsis mutant sgs3 was recently cloned and was not found to have similarity to any other known protein. By a detailed analysis of the sequence of SGS3 we have defined three new protein domains: the XH domain, the XS domain and the zf-XS domain, that are shared with a large family of uncharacterised plant proteins. This work implicates these plant proteins in PTGS.ConclusionThe enigmatic SGS3 protein has been found to contain two predicted domains in common with a family of plant proteins. The other members of this family have been predicted to be transcription factors, however this function seems unlikely based on this analysis. A bioinformatics approach has implicated a new family of plant proteins related to SGS3 as potential candidates for PTGS related functions.
Highlights
ResultsThe gene for the Post transcriptional gene silencing (PTGS) impaired Arabidopsis mutant sgs was recently cloned and was not found to have similarity to any other known protein
Post transcriptional gene silencing (PTGS) is a recently discovered phenomenon that is an area of intense research interest
After initial PSI-BLAST searches with the sequence of SGS3, weak matches were found to a number of plant proteins
Summary
After initial PSI-BLAST searches with the sequence of SGS3, weak matches were found to a number of plant proteins. Using residues 85 to 225 of a weakly matching Sorghum bicolor protein (SWISSPROT accession O48878) as a PSI-BLAST [6] query at the NCBI site, using an inclusion E-value of 0.002, SGS3 was found in the second round with an E-value of 0.001. This search found a number of other plant proteins including the rice gene X product ( known as gene X1) [7]. An alignment of the Nterminal cluster is shown in figure 3 This pattern of conservation suggests a zinc binding domain. An RNA binding function would seem plausible if this larger family of proteins were involved in PTGS as the SGS3 protein appears to be
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