Several Isoforms for Each Subunit Shared by RNA Polymerases are Differentially Expressed in the Cultivated Olive Tree (Olea europaea L.)

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.

A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning‐expressed responses

“…Although only measured at the transcriptional level, this increase in the abundance of RNAP II subunits might indicate that RNAP II is more active, or, if these are subunits shared with RNAP IV, that RNAP IV is more active, supporting why there is an observed increase in global transcripts when using the RNA spike‐in method. Several publications indicate that the expression of genes encoding the RNAP subunits is affected by abiotic stress and some are required for abiotic stress tolerance (Borsani et al., 2005; Fernández‐Parras et al., 2021; Popova et al., 2013). This provided a possibility that the sorghum produces more RNAP subunits at night to reprogram gene expression in response to temperature changes, and the RNA spike‐in normalization identified additional nighttime up‐regulated RNAP coding genes.…”

Transcriptomic Insight into the Pollen Tube Growth of Olea europaea L. subsp. europaea Reveals Reprogramming and Pollen-Specific Genes Including New Transcription Factors

“…Most pollen research has been conducted on model systems, but there is still a place for non-model systems such as olive tree ( Olea europaea L. subsp. europaea ), where research on floral biology has been principally horticultural in orientation [ 31 ], and relevant and high-throughput technologies have been applied recently [ 32 , 33 , 34 , 35 , 36 , 37 ]. Olive is an emblematic and dominant crop in the Mediterranean basin whose relevance is related to the high agricultural and nutraceutical value of the fruits (olives), the landscape shaping, and more recently, its use as a source for renewable biomaterials and fuel [ 38 ].…”

RNA polymerases IV and V are involved in olive fruit development

“…In addition, there are other subunits that are common to RNA pol IV and V, but are conserved in RNA pol II, such as the subunits NRPDE2 and NRPB2, RNPDE4 and NRPB4, and NRPDE7 and NRPB7, which are shared by RNA pol IV and V and conserved with RNA pol II [5,22,[25][26][27]. Furthermore, several isoforms of the common subunit five, shared by all the RNA pols have been described, while a specific isoform, NRPE5, has been found for RNA pol V [28]. In addition, several paralogues have been described for these and other subunits in different plants [22,25,26,[28][29][30].…”

“…Furthermore, several isoforms of the common subunit five, shared by all the RNA pols have been described, while a specific isoform, NRPE5, has been found for RNA pol V [28]. In addition, several paralogues have been described for these and other subunits in different plants [22,25,26,[28][29][30]. Based on the existence of these paralogues, it has been proposed that these may perform new functions or be subject to different regulation.…”

“…In this work we searched for genes that putatively encode specific subunits of RNA pol IV and V, and for those corresponding to RNA pol II, in the olive 'Picual' cultivar given its economic, agronomic and agro-ecological importance as one of the most important fruit trees in the Mediterranean Basin [28,[46][47][48]. The analysis allowed to identify paralogues for NRPD1, NRPE1 and NRPB1, NRPDE2 and NRPB2, NRPDE4 and NRPB4, NRPDE7 and NRPB7, and also for NRPB7-like, in addition to the putative pseudogenes, according to our transcriptomic analyses.…”