Mutations in retrotransposon AtCOPIA4 compromises resistance to Hyaloperonospora parasitica in Arabidopsis thaliana

Abstract

Retrotransposons (RTEs) are a principal component of most eukaryotic genomes, representing 50%-80% of some grass genomes. RTE sequences have been shown to be preferentially present in disease resistance gene clusters in plants. Arabidopsis thaliana has over 1,600 annotated RTE sequences and 56 of these appear to be expressed because of the exact expressed sequence tag (EST) matches and the presence of intact open reading frames. Of the 22 represented in the Affymetrix ATH1 array, AtCOPIA4 was found to be expressed at a higher level than all other RTEs across different developmental stages. Since AtCOPIA4 is located in the RPP5 gene cluster and is adjacent to RPP4 which confers resistance to the downy mildew oomycete Hyaloperonospora parasitica isolate EMWA1, we evaluated AtCOPIA4 mutants for resistance to this pathogen. T-DNA insertional and antisense knockout of AtCOPIA4 was found to reduce the resistance of wild type plants by 2-4 folds. Our results suggest that retrotransposon can be exapted to participate in plant defense response.

Antagonistic Actions of FPA and IBM2 Regulate Transcript Processing from Genes Containing Heterochromatin

“…IBM2 promotes the transcription of the methylated Copia element AT4G16870 (Duan et al, 2017), which is a non-intronic transposon localized upstream of the RPP4 resistant gene ( Figure 6A). A chimeric RPP4-AT4G16870 mRNA consisting of both RPP4 and this Copia element (Wang and Warren, 2010) was detected in the wild type but not in ibm2-4, aipp1-1, edm2-4, or suvh456 ( Figure 6B and Supplemental Figure S7A), confirming that the transcription of RPP4-AT4G16870 is promoted by an EDM2/AIPP1/IBM2 complex and relies on the presence of heterochromatic marks controlled by SUVH proteins. Similarly, RPP4-AT4G16870 mRNAs were not detected in fpa-11 ibm2-4 mutants but were expressed in fpa-11 ( Figure 6B).…”

“…(B) Expression analysis of RPP4, AT4G16870, and the chimeric RPP4-AT4G16870 transcripts in Col-0 and different mutant backgrounds. cDNAs were amplified using primers indicated in (A) and described previously (Wang and Warren, 2010). ATEF cDNA amplifications served as controls.…”

Dynamic Roles for Small RNAs and DNA Methylation during Ovule and Fiber Development in Allotetraploid Cotton

“…Transcription initiates from TEs through Pol II or Pol IV (a homolog of Pol II) and then spreads to nearby genes [ 2 , 47 ]. While most TEs are transcriptionally silenced in plant genomes, some TEs could activate nearby genes, as reported in Arabidopsis [ 46 , 48 ] and rice [ 49 ]. If TE activation occurs prior to the transcription of nearby genes, TE expression should not be correlated with the distance between TEs and genes.…”

siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass

“…5 c). This could be attributed to TEs located close to or within the promoters of nearby genes [ 77 , 78 ]. It is possible that RNA polymerase II- or IV-mediated transcription, which is initiated by TEs, can spread to the nearby gene regions and subsequently increase expression of the nearby genes [ 46 , 79 ].…”