Abstract
Plants contain five nuclear RNA polymerases, with RNA pols IV and V in addition to conserved eukaryotic RNA pols I, II, and III. These transcriptional complexes share five common subunits, which have been extensively analyzed only in yeasts. By taking advantage of the recently published olive tree cultivar (Olea europaea L. cv. Picual) genome, we performed a genome-wide analysis of the genomic composition corresponding to subunits common to RNA pols. The cultivated olive tree genome is quite complex and contains many genes with several copies. We also investigated, for the first time, gene expression patterns for subunits common to RNA pols using RNA-Seq under different economically and biologically relevant conditions for the cultivar “Picual”: tissues/organs, biotic and abiotic stresses, and early development from seeds. Our results demonstrated the existence of a multigene family of subunits common to RNA pols, and a variable number of paralogs for each subunit in the olive cultivar “Picual.” Furthermore, these isoforms display specific and differentiated expression profiles depending on the isoform and growth conditions, which may be relevant for their role in olive tree biology.
Highlights
Gene expression is a highly regulated process that comprises coordinated steps to ensure appropriate RNA levels and to allow cells to correctly respond and adapt to any situation
By using Arabidopsis NRPA/D5 as a query, we identified three putative genes coding for the “Picual” olive homolog subunits with identities falling within the 74–79% range
The NRPE5 subunit maintained the short N-terminal extension described for the plant NRPE5, as compared to NRPA/ D5 (Supplemental Figure S2), which was suggested to be important for protein stability in vivo in Arabidopsis (Ream et al, 2009)
Summary
Gene expression is a highly regulated process that comprises coordinated steps to ensure appropriate RNA levels and to allow cells to correctly respond and adapt to any situation. Transcription is the most widely studied step in gene expression that is carried out by RNA polymerases (RNA pols). Archaea and eukarya RNA pols are heteromultimeric complexes responsible for the specific synthesis of different RNA types (Werner and Grohmann, 2011). Most eukaryotes possess three heteromultimeric RNA polymerases, namely, RNA pol I, RNA pol II, and RNA pol III ( known as RNA pols A, B, and C in plants). Plants contain two additional RNA pols—RNA pols IV and V (or RNA pols D and E)—that play roles in epigenetic regulation. They synthesize siRNAs that play roles in transcriptional silencing via RNA-directed
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