7 publications mentioning sly-MIR397

Open access articles that are associated with the species Solanum lycopersicum and mention the gene name MIR397. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

1

In the stamen library, a total of 34 unique known and 35 unique novel miRNAs showed differential expression, of which seven known (miR398a-5p, miR395a, miR398b-3p, miR397–5, pmiR160a-3, pmiR162a-5p and miR156e-3p) and seven novel miRNAs were significantly downregulated after 2 d of high-temperature treatment, whereas 31 known and 34 novel miRNAs were significantly down-regulated after 12 d of treatment (Additional file 1: Table S2 and Table S4).

qRT-PCR analysis showed that the strong downregulation of miR397–5p at 2 d in stamens and pistils was negatively correlated with changes in the expression of SlLAC4 (Fig.   8, Additional file 2: Figure S4).

In the pistil library, a total of 20 known and 10 novel miRNAs showed differential expression, of which two known miRNAs (miR398b-3p and miR397–5p) were significantly downregulated under heat stress for 2 d, and other miRNAs were detected at 12 d (Additional file 1: Table S2 and Table S4).

The expression levels of miR156e-5p, miR160a, miR393-5p, miR397–5p, miR398b-3p, and pc-7b (pc: predicted candidates of novel miRNA) showed significant reduction at 2 d after high-temperature treatment, although these miRNAs exhibited no differential expression at the later stages.

In addition, miR395a, miR397–5p, miR398b-3p, and pc-27 were markedly downregulated at 2 d after heat-stress treatment, whereas miR397–5p and miR398b-3p were strongly increased at 12 d after heat-stress treatment.

RLM-5′ RACE validated that miR398b-3p, miR393-5p, miR160a, and miR156e-5p were active and directed the cleavage of their targets, except for miR397–5p (data not shown).

Among these miRNAs, miR398b-3p, miR393-5p, miR160a, miR156e-5p, and miR397–5p were of particular interest as their predicted targets play crucial roles in plant signal transduction, flower development, and cell wall architecture [21, 41, 60, 61].

Computational analyses combined with experimental approaches provided evidence that the miR398b-3p/ SlCSD1, miR393-5p/ SlTIR1, miR160a/ SlARF10/16, miR156e-5p/ SlSPL15, and miR397–5p/ LACs cleavage cascades were tightly correlated with the regulation of the response to heat stress and metabolic pathways in stamens and pistils (Fig.   10).

However, six miRNA families, namely, miR394, miR395, miR397, miR1918, miR4376 and miR6022, had only one member (Fig.   3).

However, no cleavage sites of miR397–5p were detected in SlLAC4 transcripts in either stamens or pistils using RLM-5′-RACE.

In our study, SlLAC4 was also predicted to be cleaved by miR397–5p (Additional file 1: Table S8).

Whereas two miRNAs, miR397–5p and miR398b-3p, were common in the stamen and pistil libraries at 2 d after heat-stress treatment, 12 known miRNAs belonging to the miR159, miR160, miR319, miR393, miR482, miR1918, miR6026, and miR6027 families (Fig.   5a, Additional file 1: Table S5) were common at 12 d after heat-stress treatment.

2

miRNA Fold (↑ or ↓) Target protein class Function References miR160 ↓, 2X Auxin response factors Hormone signaling and plant development[50] miR162 ↑, 2X Dicer-like (DCL) protein Plant development[39] miR168 ↑, 2X ARGONAUTE (AGO) protein Plant development[40, 51] miR169 ↓, 2X CBF HAP2-like factors Abiotic stress responses[52] miR171 ↓, 2X Scarecrow- like (GRAS domain) TFs Flowering time[11] miR172 ↑, ~4X APETALA-2 (AP2) like TFs Floral identity and phase transition[13, 17] miR319 ↑, ~4X TCP, bHLH TF Leaf patterning[19] miR391 ↓, 3X Not known Not known miR396 ↑, 2X GRL TFs, Rhodanase like proteins Defense responses[23] miR397 ↑, 1.5X Laccases, b -6 tubulin Fungal infection[7, 23] miR398 ↑, 3X Copper superoxide dismutases (CSD1/2) Abiotic stress[43] miR408 ↑, 1.5X Plantacyanin Stress responses[23] miR447 ↑, 2.5X 2-Phosphoglycerate kinase Metabolic pathway[7]The relative expression values of the individual miRNAs as revealed from the array analysis have been plotted as a histogram (see Additional file 1; Fig. S 2 a, b).

miRNA Fold (↑ or ↓) Target protein class Function References miR160 ↓, 2X Auxin response factors Hormone signaling and plant development[50] miR162 ↑, 2X Dicer-like (DCL) protein Plant development[39] miR168 ↑, 2X ARGONAUTE (AGO) protein Plant development[40, 51] miR169 ↓, 2X CBF HAP2-like factors Abiotic stress responses[52] miR171 ↓, 2X Scarecrow- like (GRAS domain) TFs Flowering time[11] miR172 ↑, ~4X APETALA-2 (AP2) like TFs Floral identity and phase transition[13, 17] miR319 ↑, ~4X TCP, bHLH TF Leaf patterning[19] miR391 ↓, 3X Not known Not known miR396 ↑, 2X GRL TFs, Rhodanase like proteins Defense responses[23] miR397 ↑, 1.5X Laccases, b -6 tubulin Fungal infection[7, 23] miR398 ↑, 3X Copper superoxide dismutases (CSD1/2) Abiotic stress[43] miR408 ↑, 1.5X Plantacyanin Stress responses[23] miR447 ↑, 2.5X 2-Phosphoglycerate kinase Metabolic pathway[7] The relative expression values of the individual miRNAs as revealed from the array analysis have been plotted as a histogram (see Additional file 1; Fig. S 2 a, b).

, miR395, miR397 and miR399 were up-regulated both in leaves and flowers (Figure 5a and 5b) while pre-miR159 and pre-miR171 were down-regulated by 2 folds in flower tissues (Figure 5b).

Most of the miRNAs listed in the heat map were up-regulated with statistical significance and these include miR162, miR168, miR172, miR319, miR396, miR397, miR398, miR408 and miR447 (Figure 2).

The precursors of miR162, miR172, miR395, miR397 and miR399 were induced to more than five folds in ToLCNDV infected leaves, while those of miR159, miR160, miR167 and miR319 showed almost 2-3 times increase in ToLCNDV infected leaves (Table 3).

3

On the other hand, other miRNAs, such as miR161, miR173, miR393, miR397, miR398 and miR414, were expressed at relatively lower levels and can only be detected in mature green stage, Particularly, the expression levels of miR159 decreased at the breaker stage and increased at red ripening stage compared with that of the mature green stage which reveals its probable specific roles in fruit ripening or ethylene pathway, as one of the predicted targets is 1-aminocyclopropane -1-carboxylate synthase which is a crucial enzyme in ethylene biosynthesis [17].

Other conserved miRNAs targets include F-box protein (miR394, miR414), ATP sulfurylase (miR395), Pectate Lyase (miR482), endo-1, 4-beta- glucanase (miR396), Laccase (miR397), all of which are involved in regulation of metabolic processes.

4

In our present study, homologs of miR162, miR164, miR166, and miR397 were identified as significantly differentially expressed between grafted and control tomato fruits but not in the shoot tissues (Table S7).

Some miRNAs such as, miR156, miR162, miR164, miR166, miR172, miR397, and miR398 were reported to be highly conserved in tomato fruit and developmental stages (Zuo et al., 2012; Karlova et al., 2013).

At the same time, MIR397, MIR5302, MIR8007 has infrequently sequenced.

5

Some target genes of the conserved miRNAs encode drought-stress related proteinase, such as the targets of sly-miR396 and sly-miR397, which encode cysteine proteinase and laccase, respectively.

6

In the current study, sha-miR397(sha-miR397_nta and sha-miR397-p5) and sha-miR319 (sha-miR319 and sha-miR319b_stu) were both found to be induced by chilling stress, which indicated that some miRNAs involved in chilling stress showed consistency among several plant species.

Among these miRNAs, 12 miRNAs that were sha-miR166a-p5, sha-miR319, sha-miR397_nta, sha-miR397-p5, sha-miR398a-3p_stu, sha-miR398a-5p_stu, sha-miR398a-p3_cme, sha-miR399-p5, sha-miR408_nta, sha-miR408a-3p_stu, sha-miR408b-5p_stu and sha-miR530a_cme significantly increased in response to chilling stress, while 20 miRNAs significantly decreased (Additional file 1: Table S1).

7

MiR171 and miR397 are associated with nodule infection and the nitrogen-fixing ability of Lotus japonicus (De Luis et al., 2012).