8 publications mentioning ptc-MIR156a

Open access articles that are associated with the species Populus trichocarpa and mention the gene name MIR156a. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

1

In order to know miR156-medicated posttranscriptional regulation of PtSPLs, we searched coding regions and 3’ UTRs of all PtSPLs for targets of P. trichocarpa miR156a–miR156j on the psRNATarget server using default parameters [45].

PtSPLs targeted by miR156 were predicted by searching the coding regions and 3’ UTRs of all PtSPLs for complementary sequences of P. trichocarpa miR156a–miR156j on the psRNATarget server using default parameters [45] (http://plantgrn.

Motif 14 existed in G1 and G2 SPLs contains the target gene sequence of miR156, indicating the posttranscriptional regulation of G1 and G2 SPLs by miR156.

Target prediction showed that all PtSPLs in groups 1, 2 and 5 were regulated by miR156.

OsSPLs targeted by miR156 are involved in the development of flowers in rice.

Prediction of PtSPLs targeted by miR156.

In addition, 18 of the 28 PtSPLs, belonging to G1, G2 and G5, were found to be targets of miR156.

The results showed that 18 PtSPLs were potential targets of miR156 (Figures  9 and 10).

Six AtSPLs, including AtSPL1, AtSPL7, AtSPL8, AtSPL12, AtSPL14 and AtSPL16, are not targets of miR156 in Arabidopsis.

MiR156 -mediated posttranscriptional regulation of PtSPLsIt has been shown that 10 AtSPLs are regulated by miR156 [11].

Consistently, AtPSLs clustering in G1, G2 and G5 are targets of miR156 in Arabidopsis.

Figure 10 PtSPLs targeted by miR156.

Prediction of PtSPLs targeted by miR156The sequences of P. trichocarpa miR156a–miR156j were obtained from miRBase [36] (http://www.

MiR156 -targeting sites in 13 PtSPLs belonging to G1 and G2 locate in the last exon and encode the conserved peptide ALSLLS.

Through comprehensive analyses of gene structures, phylogenetic relationships, chromosomal locations, conserved motifs, expression patterns and miR156 -mediated posttranscriptional regulation, the PtSPL gene family was characterized.

It is consistent with the results from Arabidopsis SPLs and suggests the conservation of miR156 -mediated posttranscriptional regulation in plants.

It suggests that miR156 -mediated posttranscriptional regulation of SPLs is conserved in P. trichocarpa and Arabidopsis.

Ten of the 16 AtSPLs, including AtSPL2– AtSPL6, AtSPL9– AtSPL11, AtSPL13 and AtSPL15, are regulated by miRNAs belonging to the MIR156 family [11- 17].

Consistently, all of the AtSPLs in these groups are regulated by miR156.

It suggests the conservation of miR156 -mediated posttranscriptional regulation in plants.

However, the regulation of miR156 in P. trichocarpa PtSPLs has not been analyzed.

It has been shown that 10 AtSPLs are regulated by miR156 [11].

OsSPL14 regulated by miR156 also controls shoot branching in the vegetative stage [8, 28, 29].

The complementary sites of miR156 are in the coding regions or 3’ UTRs of AtSPLs.

The complementary sites of miR156 locate in the coding region of G1 and G2 SPLs, whereas it locates in 3’ UTR of G5 SPLs.

Through a comprehensive analysis of gene structures, phylogenetic relationships, chromosomal locations, conserved motifs, expression patterns and miR156 -mediated posttranscriptional regulation, the PtSPL gene family was characterized and compared with SPLs in Arabidopsis.

A total of 352 miRNA precursors, including 12 for miR156, have been identified [33- 39].

The sequences of P. trichocarpa miR156a–miR156j were obtained from miRBase [36] (http://www.

Figure 9 Sequence alignment of P. trichocarpa miR156a–miR156j with their complementary sequence in coding regions and 3’ UTRs of 18 PtSPLs.

MiR156-medicated posttranscriptional regulation is important for the function of a subset of SPLs[11, 41, 65].

MiR156 -mediated posttranscriptional regulation of PtSPLs.

AtSPL3, AtSPL4 and AtSPL5 contain complementary sequences of miR156 in 3’ UTR, and all of them promote vegetative phase change and flowering [10, 14, 18].

2

For example, the target genes of miR156 and miR1448 encoded plant disease resistance proteins (NBS-LRR proteins); two targets of miR164 encoded LRR defense proteins and TMV-resistance proteins; one target of miR398 and miR159 encoded two pathogenesis-related proteins, CSD and peroxidase (POD), respectively; and one target of miR159 encoded cytokinin oxidase (CKX) family proteins.

For instance, the targets of miR156 and miR160 were genes encoding squamosa promoter -binding (SPB) proteins; the target genes of miR166 encoded a homeodomain-leucine zipper protein (HD-ZIP); and miR159, miR164, and miR319 targeted myeloblastic leukemia (MYB) factors.

The targets of miR156 and miR160 were genes encoding ARF, whereas miR164 and miR166 both targeted NAC domain proteins.

Moreover, viruses or viral suppressors also switch on the expression of tobacco miR156 [36] and Arabidopsis miR156 [37].

For example, expression of miR156, miR160, miR164, miR166, miR168, miR398, and miR408 increases while miR159 shows reduced expression after UV-B radiation in P. tremula [10].

In total, 15 qPCR validation reactions (designed for detecting the expression of miR156, miR159, miR160, miR164, miR166, miR168, miR172, miR319, miR398, miR408, miR1448, and miR1450) for the 41 fungi-response miRNAs tested were carried out.

Group II contained miR156, miR160, miR164, miR1448, miR398, miR408, and three members of miR166; expression of these miRNAs was always higher at 5 DAI than that at 3 or 7 DAI.

The most interesting discovery in this study was that miR156 responded to all six of the above stresses in Populus, although the expression patterns differed in response to cold, mechanical, drought, dehydration, and fungal invasion stresses.

MiR156, miR159, miR160, miR164, miR168, miR172, and miR408 are significantly expressed in tension- and compression-stressed developing xylem of P. trichocarpa [12], and miR156, miR160, miR164, and miR168 also respond to cold stress in P. trichocarpa [4].

Together, we infer that miR156 could be an integral component of the miRNA -mediated gene expression response to environmental stresses (signals) in plants.

In P. euphratica, miR156, miR164, and miR408 are differentially expressed under dehydration stress [22], and miR156, miR319, and miR166 respond to drought stress [21].

In addition, miR156 is considered an evolutionarily conserved regulator of vegetative phase change in both annual herbaceous plants and perennial trees [38], accompanied by miR172, where miR156 controls the transition from juvenile to adult development [39], [40].

Other TF-related feedback regulatory networks are the miR156-SPL interaction in Arabidopsis [40], and miRNA-WRKY in rice, maize, and Arabidopsis [47], [56], [61].

In these diverse examples, miR156 and miR164, two miRNAs that respond to many environmental stresses, are both involved in the miRNA-TF feedback regulatory network, suggesting their key roles in stress responses.

Among these miRNAs, several also respond to pathogenic fungi in other plants, for example, miR156, miR159, miR160, and miR319 in galled loblolly pine stem infected with C. quercuum f. sp.

fusiforme, miR156, miR159, miR164, and miR396 in wheat leaves infected with two powdery mildew pathogens of E. graminis f. sp.

These probes belong to 12 miRNA families (miR156, miR159, miR160, miR164, miR166, miR168, miR172, miR319, miR398, miR408, miR1448, and miR1450) and account for 17.52% of the 234 probes.

Among those miRNAs, miR156 responded to all stresses, suggesting it might be an integral component of miRNA pathways for all biotic and abiotic stresses in Populus.

The miR156 is an Integral Component of miRNA Pathways for all Biotic and Abiotic Stresses in Plants.

In other plants, miR156 was also reported to respond to several kinds of biotic and abiotic stress.

The level of miR156 significantly decreases/increases in phosphate-deprived and temperature-stressed Arabidopsis [30], [31], in dehydration-stressed Hordeum vulgare (barley) [32], in drought-challenged rice [33], in domesticated durum wheat (Triticum turgidum ssp.

Moreover, 172 miR156 molecules found in 24 species, both gymnosperms and angiosperms, are in release 18 of the miRBase (http://www.

The ubiquitous distribution, evolutionary conservation, and crucial roles in biological rhythms suggest that miR156 might play a key role in the transition between differential physiological stages or phases.

In addition, miR156 is significantly repressed in galled loblolly pine stems infected with the fungus C. quercuum f. sp.

Similar to miR156, miR164 also responds to different stresses in diverse plants [4], [5], [10], [12], [22], [35], [36], [37].

3

Consequently, we predicted 25 target genes for Pto-miR156, Pto-miR159, Pto-miR172 and Pto-miR319 that were different from the previously defined Populus miRNA targets (miRBase 19.0), and a total of 464 targets were identified for the 78 novel miRNAs (Table S3).

Target Prediction for Pto-miR156, Pto-miR159, Pto-miR172 and Pto-miR319 and Novel miRNAs in Andromonoecious P. tomentosa To understand the functions of sex-specific flower development related miRNAs, the first step is to predict and experimentally validate their targets.

By contrast, miRNA156 was expressed in male flower at higher levels than in female flower.

Target Prediction for Pto-miR156, Pto-miR159, Pto-miR172 and Pto-miR319 and Novel miRNAs in Andromonoecious P. tomentosa.

Several miRNA families, such as miR156, miR159, miR169, miR319, miR396, and miR1447, had moderate expression levels (Table 2).

For example, three miRNA families (miR172, miR159/miR319 and miR156) are involved in flowering-time regulation [27].

miRNA156, miRNA157 and miRNA172 may be components of a regulatory pathway mediating the transition between the vegetative and reproductive phases in plants [28].

4

The ten most highly expressed miRNAs (miR156, miR157, miR159, miR164, miR167, miR172, miR393, miR396, miR414, miR2275, and miR5021) in buds and leaves are miRNAs regulating genes involved in flower and leaf development processes such as integument development, leaf morphogenesis, meristem initiation, maintenance, and growth, bilateral symmetry determination, organ morphogenesis, plant phase transition, shoot apical meristem identity, flower and fruit development, and plant architecture.

miR156, miR159, miR166, miR172, miR390, miR396, and miR5021 are the most expressed families in bud tissues.

In silico expression analyses of miRNAs using DEGseq [25] identified 19 sequences belonging to eight conserved miRNA families (miR156, miR157, miR164, miR172, miR393, miR396, miR414, and miR2275) induced in winter buds versus leaves (Additional file 6: Table S6).

Most of conserved families common to Arabidopsis and peach (miR156, miR159, miR160, miR164, miR166, miR171, miR172, miR319, miR390, miR395, and miR396) did not show significant size variation (Figure 4).

miRNA families such as miR156, miR169, miR172, miR395, and miR5021 have the largest number of members with the latter having 18 members.

Three of these miRNA genes (miR156, miR172, and miR398) were also reported as responding to cold stress in several studies [4, 8, 10, 29, 30].

5

However, miR399 and miR156 were not among the differentially methylated miRNAs, excluding that these regulons are directly targeted by DNA methylation.

For instance, in many plant species, miRNA targeted genes are involved in a mechanistic network of plant P signaling, e. g. the miR399-PHR1-PHO2 regulon [22, 23], the miR156-SPL3-Pht1;5 pathway [24] and the miR827-NLA-P [i] homeostasis network [25].

During P starvation, miR156 is induced and therefore its target SPL3 is repressed.

In addition, miR156-SPL3-PHT1;5 pathways also constitute a component of the P deficiency -induced regulatory mechanism in Arabidopsis.

6

Not all the R3 MYB genes in Arabidopsis are activated by the TTG1–GL3/EGL3–GL1 activator complex (Wang et al., 2008), and microRNA156 (MIR156) -targeted SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) 9 has been shown to activate TCL1, TCL2, and TRY (Yu et al., 2010; Gan et al., 2011).

Temporal control of trichome distribution by MicroRNA156 -targeted SPL genes in Arabidopsis thaliana.

7

and found only two homologous pairs based on our test: ath-MIR156a–157a and ath-MIR165a–166a.

As a positive case, we classify the three miR172a miRNAs from Arabidopsis, Oryza, and Populus as homologs (the same is true for miR156a—no other similar cases were explored).

In Arabidopsis, only the miR171 family is divided in two families, and the following miRBase families are pairwise grouped together: MIR319–MIR159, MIR156–MIR157, MIR165–MIR166, and MIR170–MIR171.

As a negative test case, we took 21 Arabidopsis “a” precursors (ath-MIR156a, ath-MIR157a, etc. )

8

Several Arabidopsis and rice families such as miR156/157, miR159/319, miR162, miR172, miR396, miR397, miR473, and miR475 are nearly double in size in Populus.

miR156/157, miR159 and miR319 are represented by 22 and 38 members respectively and three other families (miR169, miR170/171, miR165/166) are represented by more than 20 members.

For families miR156/157, miR159, miR319, miR162, miR172, miR396, miR397, miR473, miR475 and miR482, the number of members identified in this study was at least twice that reported previously [3, 26] (Fig. 2).