The SGS3 protein involved in PTGS finds a family
© Bateman; licensee BioMed Central Ltd. 2002
Received: 11 July 2002
Accepted: 5 August 2002
Published: 5 August 2002
Post 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.
The 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.
The 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.
Post transcriptional gene silencing (PTGS) is a recently discovered phenomenon . The components of PTGS are being cloned and experiment combined with sequence analysis is helping to elucidate its mechanisms. Study of PTGS is providing links between diverse biological processes such as defence against viruses, RNA metabolism [2, 3] and development . The gene for the PTGS impaired Arabidopsis mutant sgs3 was recently cloned . An initial analysis of the protein did not reveal any motifs, domains or similarity to any other protein. To help shed light on the function of SGS3 a more detailed analysis of the protein has been carried out.'
After initial PSI-BLAST searches with the sequence of SGS3, weak matches were found to a number of plant proteins. Reciprocal matches can often verify the significance of weak matches. Using residues 85 to 225 of a weakly matching Sorghum bicolor protein (SWISSPROT accession O48878) as a PSI-BLAST  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 also found a number of other plant proteins including the rice gene X product (also known as gene X1) .
After initial alignment of the protein sequences the DNA sequence for each was inspected for possible frameshift errors and incorrect splicing boundaries using tblastn and genewise.
The XS domain containing proteins are predicted by ncoils  to contain coiled-coils, which suggests that they will oligomerise. Most coiled-coil proteins form either a dimeric or a trimeric structure. It is possible that different members of the XS domain family could oligomerise via their coiled-coils forming a variety of complexes.
Can we infer the function of SGS3 based on its similarity to other XS domain proteins? Unfortunately the members of this family are functionally uncharacterised. However, rice gene X was predicted by Chen et al. to be a transcription factor based on two pieces of evidence: (i) the presence of the coiled-coil as found in other transcription factors such as GCN4 , (ii) the rice gene X contains a ring zinc finger . However, many coiled-coils are found in non-transcription factor proteins weakening the first argument. Ring fingers are now thought to mediate the protein interactions of ubiquitin ligases rather than interact with DNA . The Rice gene X is the only member of this family that contains a ring finger. This second piece of evidence no longer points to a transcription factor function, but potentially to a role in ubiquitination. Therefore the evidence used to infer these protein are transcription factors is weak and the inference unlikely to be correct.
In summary this analysis suggests that SGS3 may have a nucleic acid binding function and that a large family of plant proteins containing the novel XS and XH domains may be uncharacterised components in PTGS.
AB is supported by the Wellcome Trust. I would like to thank William Mifsud, Richard Durbin for comments on the manuscript.
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