Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II.
In addition to RNA polymerases I, II, and III, the essential RNA polymerases present in all eukaryotes, plants have two additional nuclear RNA polymerases, abbreviated as Pol IV and Pol V, that play nonredundant roles in siRNA-directed DNA methylation and gene silencing. We show that Arabidopsis Pol IV and Pol V are composed of subunits that are paralogous or identical to the 12 subunits of Pol II. Four subunits of Pol IV are distinct from their Pol II paralogs, six subunits of Pol V are distinct from their Pol II paralogs, and four subunits differ between Pol IV and Pol V. Importantly, the subunit differences occur in key positions relative to the template entry and RNA exit paths. Our findings support the hypothesis that Pol IV and Pol V are Pol II-like enzymes that evolved specialized roles in the production of noncoding transcripts for RNA silencing and genome defense.
Ream
Thomas S
TS
Biology Department, Washington University, St. Louis, MO 63130, USA.
Haag
Jeremy R
JR
Wierzbicki
Andrzej T
AT
Nicora
Carrie D
CD
Norbeck
Angela D
AD
Zhu
Jian-Kang
JK
Hagen
Gretchen
G
Guilfoyle
Thomas J
TJ
Pasa-Tolić
Ljiljana
L
Pikaard
Craig S
CS
D000595:Amino Acid Sequence; D029681:Arabidopsis Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D018744:DNA, Plant / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020868:Gene Silencing; D008954:Models, Biological; D008969:Molecular Sequence Data; D010802:Phylogeny; D030821:Plants, Genetically Modified; D021122:Protein Subunits / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D034622:RNA Interference; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000378:metabolism; D022661:RNA, Untranslated / Q000378:metabolism; D016415:Sequence Alignment
D029681:Arabidopsis Proteins; D018744:DNA, Plant; D021122:Protein Subunits; D034741:RNA, Small Interfering; D022661:RNA, Untranslated; D012319:RNA Polymerase II; C499181:RNA polymerase IV, Arabidopsis; C538841:RNA polymerase V, Arabidopsis; D012321:DNA-Directed RNA Polymerases