Engineered ripening-specific accumulation of polyamines spermidine and spermine in tomato fruit upregulates clustered C/D box snoRNA gene transcripts in concert with ribosomal RNA biogenesis in the red-ripe fruit

Authors: SHUKLA, VIJAYA - Former ARS Employee; FATIMA, TAHIRA - Purdue University; GOYAL, RAVINDER - Agriculture And Agri-Food Canada; HANDA, AVTAR - Purdue University; Mattoo, Autar

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/2/2020
Publication Date: 12/4/2020
Citation: Shukla, V., Fatima, T., Goyal, R.K., Handa, A.K., Mattoo, A.K. 2020. Engineered ripening-specific accumulation of polyamines spermidine and spermine in tomato fruit upregulates clustered C/D box snoRNA gene transcripts in concert with ribosomal RNA biogenesis in the red-ripe fruit. Plants. 9:1710. https://doi.org/10.3390/plants9121710.
DOI: https://doi.org/10.3390/plants9121710

Interpretive Summary: Polyamines such as spermidine and spermine have emerged as new plant hormones. Their expression is highly controlled in living cells. In plants they have been shown to prolong life to fruits and leaves as well as combat abiotic stress. We developed high spermidine/spermine tomatoes which give higher yield, have a prolonged life span and produce nutrients for human consumption. The mechanistic details about how these plant hormones help achieve these positive attributes in fruits are not well known nor understood until now. We demonstrate here the entire cellular pathways positively impacted by spermidine/spermine that are specific and involve induction of small nucleolar ribosomal nucleic acids (snoRNA) in the innermost organ in a cell called nucleolus. This induction in turn results in the plants ability to upregulate hundreds of genes involved in protein synthesis. All these genes were catalogued and related to the protein pathways that were upregulated. This study provides novel information about the nexus between spermidine/spermine and snoRNAs to positively impact plant life, including resistance against abiotic stress, and will be a valuable new vista for plant physiologists, biotechnologists and genetic experts.

Technical Abstract: Ripening of tomato fruit leads to sequential decrease in the endogenous levels of polyamines spermidine (SPD) and spermine (SPM) while the trend for the diamine putrescine (PUT) levels is generally an initial decrease followed by a substantial increase thereafter reaching high levels at the red-ripe fruit stage. Genetic engineering fruit-specific expression of heterologous yeast S-adenosylmethionine (SAM) decarboxylase in tomato resulted in high accumulation of SPD and SPM at the cost of PUT. We hypothesized that biogenic amines SPD and SPM positively impact protein synthesis by influencing biogenesis, transcription, processing and stability of ribosomal RNA (rRNA) genes in tomato fruit. One major biogenetic process regulating transcription and processing of pre-mRNA complexes in the nucleus involves the role of small nucleolar RNAs (snoRNAs) and likely the polyamines. We cloned, sequenced and identified a box C/D snoRNA cluster in tomato, namely, SlSnoR12, SlU24a, Slz44a, Slz132b. Similar to this snoRNA cluster housed on Chr. 6, two other noncoding C/D box genes SlsnoR12.2 and SlU24b with a 94% identity to those on Chr. 6 were found located on Chr. 3. Other snoRNAs divisible into snoRNA subcluster A and snoRNA subcluster B, separated by a uridine rich spacer, were decorated with other C/D box snoRNAs, namely, J10.3, Z131a/b, J10.1, Z44a followed by z132a, J11.3, z132b, U24, Z20, U24a and J11. Several of these, for example, SlZ44a, Slz132b and SlU24a, share conserved sequences like those in Arabidopsis and rice. RNAseq analysis showed significant enrichment of RNA polymerases, ribosomal, and translational proteins in high SPD/SPM transgenic tomatoes at breaker+8 stages as compared to 556AZ control. Thus, these results indicate that SPD/SPM regulate snoRNA and rRNA expression directly or indirectly, in turn affecting protein synthesis, metabolism and other cellular activities in a positive manner.