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

Abstract

Ripening of tomato fruit leads, in general, to a 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, and thereafter reaching high levels at the red ripe fruit stage. However, genetic engineering fruit-specific expression of heterologous yeast S-adenosylmethionine (SAM) decarboxylase in tomato has been found to result in a high accumulation of SPD and SPM at the cost of PUT. This system enabled a genetic approach to determine the impact of increased endogenous levels of biogenic amines SPD and SPM in tomato (579HO transgenic line) and on the biogenesis, transcription, processing, and stability of ribosomal RNA (rRNA) genes in tomato fruit as compared with the non-transgenic 556AZ line. One major biogenetic process regulating transcription and processing of pre-mRNA complexes in the nucleus involves small nucleolar RNAs (snoRNAs). To determine the effect of high levels of SPD and SPM on these latter processes, we cloned, sequenced, and identified a box C/D snoRNA cluster in tomato, namely, SlSnoR12, SlU24a, Slz44a, and Slz132b. Similar to this snoRNA cluster housed on chromosome (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. We also found that other snoRNAs divisible into snoRNA subclusters A and B, separated by a uridine rich spacer, were decorated with other C/D box snoRNAs, namely, J10.3, Z131a/b, J10.1, and Z44a, followed by z132a, J11.3, z132b, U24, Z20, U24a, and J11. Several of these, for example, SlZ44a, Slz132b, and SlU24a share conserved sequences similar to those in Arabidopsis and rice. RNAseq analysis of high SPD/SPM transgenic tomatoes (579HO line) showed significant enrichment of RNA polymerases, ribosomal, and translational protein genes at the breaker+8 ripening stage as compared with the 556AZ control. Thus, these results indicate that SPD/SPM regulates snoRNA and rRNA expression directly or indirectly, in turn, affecting protein synthesis, metabolism, and other cellular activities in a positive manner.

Comprehensive Genome-Wide Analysis and Expression Pattern Profiling of the SlHVA22 Gene Family Unravels Their Likely Involvement in the Abiotic Stress Adaptation of Tomato

“…We also identified several genes in the co-expression networks that were related to abiotic stress responses and/or expressed in fruits, such as SPS1 (Solyc07g007790), SlPDI7-2 (Solyc11g019920), SlMC8 (Solyc10g081300), SlWRKY1 (Solyc07g047960), SlWRKY3 (Solyc08g081610), Solyc07g064820 (Mitogen-activated protein kinase kinase 2-like), Solyc07g040960 (Salt responsive protein 2), and SlGPAT6 (Solyc09g014350) in the co-expression network of SlHVA22g [ 50 , 51 , 52 , 53 , 54 , 55 , 56 ]; SlRabGAP9a (Solyc07g049580), SlRabGAP21a (Solyc12g009610), SlGT-33 (Solyc12g043090), SlFdAT1 (Solyc12g088170), Solyc11g045120 (Translation initiation factor SUI1), and Solyc11g044910 (β-D-xylosidase) in that of SlHVA22k [ 57 , 58 , 59 , 60 , 61 , 62 , 63 ]; and Solyc10g078600 (phosphate transporter 1-1), C2H2 zinc finger ( C2H2-ZF ) (Solyc11g017140), Solyc11g045120 (Translation initiation factor SUI1), Solyc11g044910 (β-D-xylosidase), SlRabGAP9b (Solyc12g005930), SlRabGAP21a (Solyc12g009610), and SlFdAT1 (Solyc12g088170) in that of SlHVA22l [ 57 , 58 , 59 , 62 , 64 , 65 ] ( Figure 6 and Table S12 ). These findings suggest that these three genes, whose transcript levels were high in fruit and induced by abiotic stresses, likely function together with the co-expressed genes in the fruit development and abiotic stress response of tomato.…”

Enzymatic Spermine Metabolites Induce Apoptosis Associated with Increase of p53, caspase-3 and miR-34a in Both Neuroblastoma Cells, SJNKP and the N-Myc-Amplified Form IMR5

“…Polyamines are organic compounds having more than two amino groups, and with a role in several physiological functions, such as DNA synthesis, cellular proliferation, differentiation, and response to abiotic and biotic stresses [16][17][18][19]. Many findings have demonstrated the important properties of these polycations.…”

Update on the Roles of Polyamines in Fleshy Fruit Ripening, Senescence, and Quality

“…The importance of the PA Put in extending tomato fruit shelf life has recently come into focus, together with Spd and Spm ( Gupta et al, 2019 ; Osorio et al, 2020 ). Notably, Spd/Spm may regulate small nucleolar RNAs (snoRNAs) and ribosomal RNA (rRNA) expression directly or indirectly, which in turn will affect protein biosynthesis, metabolism, and other cellular activities in a positive manner ( Shukla et al, 2020 ).…”

“…In non-climacteric fruits, such as strawberry ( Fragaria ananassa ), ripening is largely controlled by ABA ( Li et al, 2011 ; Shen and Rose, 2014 ). In addition to ABA and ethylene, a series of studies also suggested a critical role for PAs in fruit ripening ( Dibble et al, 1988 ; Kushad et al, 1988 ; Rodriguez et al, 1999 ; Lester, 2000 ; Bregoli et al, 2002 ; de Dios et al, 2006 ; Mattoo et al, 2006 , 2007 , 2010 ; Handa and Mattoo, 2010 ; Parra-Lobato and Gomez-Jimenez, 2011 ; Koushesh saba et al, 2012 ; Gupta et al, 2013 ; Fortes et al, 2015 ; Jiang et al, 2015 ; Simpson et al, 2017 ; Guo et al, 2018 ; Liu et al, 2018 ; Shukla et al, 2020 ). In the past several years, many reviews have explored the roles of ABA and ethylene in the ripening of fleshy fruits, while a handful of reviews have reported on the roles of PAs in response to development and stress in plants ( Kusano et al, 2018 ; Chen et al, 2019 ; Fortes et al, 2019 ; Wang et al, 2019 ; Killiny and Nehela, 2020 ).…”