Identification of GROWTH-REGULATING FACTOR Transcription Factor Family Involved in Leaf Growth Regulation in Lettuce (Lactuca sativa L.)

doi:10.21203/rs.3.rs-289872/v1

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Identification of GROWTH-REGULATING FACTOR Transcription Factor Family Involved in Leaf Growth Regulation in Lettuce (Lactuca sativa L.)

https://doi.org/10.21203/rs.3.rs-289872/v1

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Background: GROWTH-REGULATING FACTORs (GRFs), a type of plant-specific transcription factors, play important roles in regulating plant growth and development. Although GRF gene family has been identified in various plant species, a genome-wide analysis of GRF gene family in lettuce (Lactuca sativa L.) has not been reported yet.

Results: Here we identified 15 members of GRF genes in lettuce and performed comprehensive analysis of them, including chromosomal locations, gene structures, and conserved motifs. Through phylogenic analysis between GRF genes in Arabidopsis and rice, we divided LsaGRFs into six groups. Specifically, the N-terminal of LsaGRF5 showed transcriptional activity, LsaGRF5 probably functioned as a transcriptional factor in cell nucleus. Meanwhile, 14 LsaGRF genes were predicted to be the target of Lsa-miR396 except of LsaGRF9 using free energies of duplex structures. LsaGRF5 could be cleaved by Lsa-miR396 at speciﬁc binding site between the 9th and 10th nucleotides. Furthermore, overexpression of LsaGRF5 in lettuce exhibited larger leaves, while smaller leaves were observed in LsaMIR396a overexpression lines, in which LsaGRF5 was down-regulated.

Conclusions: These results in lettuce provide insight into the molecular mechanism of GRF gene family in regulating leaf growth and development and foundational information for genetic improvement of the lettuce variations specialized in leaf character.

Plant Physiology and Morphology

Plant Molecular Biology and Genetics

Lettuce

GROWTH-REGULATING FACTOR

Leaf development

MicroRNA

Genome-wide analysis

As one of the plant-specific transcription factors, GROWTH-REGULATING FACTORs (GRFs) are important regulators in plant growth and development. The first identified GRF functions on gibberellic acid (GA)-induced stem elongation [1]. In various studies, the functions of GRF genes were found in development of leaf, stem, seed and root by regulating cell proliferation or cell expansion to form large organs [1–8], other new functions in flowering, stress response and plant longevity were uncovered recently [9–15]. Two conserved domains, the QLQ (Gln, Leu, Gln, IPR014978) and WRC (Trp, Arg, Cys, IPR014977) domains are found in the N-terminal of GRF family proteins [1, 2, 8, 16]. QLQ domain is considered to be a protein-protein interaction domain [1]. In yeast SWI2/SNF2 protein, the QLQ domain could facilitate the interaction with other proteins to form a complex involved in chromatin remodeling [17]. WRC domain is supposed to be involved in DNA binding and targeting of the transcription factor (TF) to the nucleus [1, 18]. Interestingly, QLQ motif containing proteins are found in all eukaryotes, while WRC domains are plant-specific [8]. Genome-wide analyses reveal that GRFs and a few bZIP transcription factors are the major targets of microRNA396 (miR396) [19].

Most Arabidopsis thalina GRF genes play important roles in leaf size control [6–8]. Overexpression of AtGRF1 and AtGRF2 respectively cause larger leaves with increased cell size, while atgrf1/2/3 triple mutant showed smaller and narrower leaves [2]. Besides functional redundancy with AtGRF1 to AtGRF3, AtGRF4 is also involved in embryonic development of cotyledons and shoot apical meristems (SAM) [4]. Overexpression of AtGRF5 exhibit bigger leaves due to increased cell number but not cell size [3]. The function of AtGRF5 could not be replaced by other AtGRFs, though some functions of them overlap [3, 12]. AtGRF9 contribute to determining final leaf size, although it has a minor role in cell proliferation [3, 20]. miR396 shares nearly perfect sequence complementarity with the transcript of WRC motif in seven members of the AtGRF genes, except for AtGRF5 and AtGRF6 in Arabidopsis thalina [21, 22]. Correspondingly, miR396a and miR396b regulate leaf growth and development by repressing the expression of AtGRFs [21, 22]. Additionally, the miR396-AtGRF module could also regulate adaxial–abaxial (Ad-Ab) polarity formation during leaf morphogenesis [23].

In addition to leaf growth regulation, GRF family is also involved in development of other tissues, such as flower organ, root and seed. BnGRF2 could increase seed weight and oil content by upregulating the expression of chloroplast-related genes in rapeseed (Brassica napus) [24]. In rice (Oryza sativa), OsGRF4 played an important role in grain weight [25, 26]. MiR396a regulates flower formation, including sepal-petal identity, by regulating the expression of GRF gene [15]. The seedlings with overexpressed miR396-resistant AtGRF1 or AtGRF3 showed shorter roots [9]. GRF proteins form functional transcriptional complex with the transcription cofactor GRF-Interacting Factors (GIF) [27], and GRF-GIF chimeras could dramatically increase the efficiency and speed of regeneration in various species [28]. These findings highlight the comprehensive roles of GRF gene family in plant growth, development and regeneration.

The ever-developing whole-genome sequencing technology, identifies GRF genes in various plant species, such as Arabidopsis thaliana [2], Oryza sativa [16], Zea mays [29], Brassica rapa [30], Solanum lycopersicum [31], Pyrus bretschneideri, Vitis vinifera [32], Brassica napus [33], Nicotiana tabacum [34] and Populus trichocarpa [35]. Lettuce (Lactuca sativa L.) is an important leafy vegetable, the leaf size of which has significant meaning for production. The whole genome sequence of lettuce cultivar ‘Salinas’ has been recently released [36]. However, the GRF gene family in lettuce has not been evaluated yet. In this study, we identified 15 GRF genes in lettuce and respectively named them based on their chromosomal location. They were divided into six groups according to evolutionary relationship with the AtGRFs. To investigate the transcriptional factor character, LsaGRF5 was specifically studied for its subcellular location and transcriptional activity. In addition, LsaGRF5 was found to be cleaved as a target of miR396. Genetically, LsaGRF5 could enhance the leaf growth in lettuce and Arabidopsis thalina when overexpressed, while smaller leaves were obtained through overexpression of Lsa-miR396 in lettuce. These results may provide a foundation for further elucidation of the function of LsaGRFs and Lsa-miR396 in leaf growth regulation in lettuce.

Identification of the GRF genes and miR396s in lettuce

To identify the GRF gene family in lettuce, the GRF genes from Arabidopsis thalina, rice and tomato were firstly used as the query sequences for BLASTP searching in lettuce genome database. Thus, thirteen candidate GRF genes were obtained in lettuce. GRF protein contains two conserved functional domains, QLQ and WRC. Therefore, QLQ (PF08880) and WRC (PF08879) were used for the Hidden Markov Model (HMM) search, and another two candidate LsaGRF genes were identified. Finally, all fifteen candidate LsaGRF genes were applied for BLASTP searching, and no further hits were got. Thus, there are totally 15 LsaGRF genes identified in lettuce genome. Based on their respective location on the chromosomes, we designated them as LsaGRF1 to LsaGRF15 respectively (Fig. 1A). LsaGRFs were distributed on each chromosome of lettuce, except for chromosome 1 and 7, and the most (five LsaGRFs) occurred on chromosome 6 (Fig. 1A). The basic information of LsaGRF1-15, including gene ID, chromosomal location, length of gene and protein, PI value and exon numbers, was listed in Table 1. Most LsaGRFs had 3 or 4 exons, except for LsaGRF4, 7 and 9 (Table 1). In addition, the predicted isoelectric point (pI) values of LsaGRF preoteins were between 6 and 9, except that the pI values of LsaGRF4 and LsaGRF7 were higher than LsaGRF9 (Table 1). The amino acid sequence alignment of 15 LasGRF was showed in Fig. S1. All of the 15 LsaGRFs contained the conserved WRC domain, but only 13 LsaGRFs had complete QLQ domain. There is no QLQ domain in LsaGRF4, and LsaGRF7 has only an incomplete QLQ domain (Fig. 1B).

The GRF genes are known as the target of miR396s. To date, two MIR396s in Arabidopsis (Ath-MIR396s) and seven MIR396s in rice (Osa-MIR396s) are identified. There are five MIR396s, MIR396a to MIR396e, in lettuce genome [36]. The evolutionary relationship between these five Lsa-MIR396s was shown in Fig. S2A based on their stem-loop sequences. The Lsa-MIR396s showed much closer evolutionary relationship with Ath-MIR396s than with Osa-MI396s (Fig. S2B). The target sequence of miR396s locates at the end of the WRC domain (Fig. 1C). Although the stem-loop structures were totally distinct, five Lsa-miR396s were highly conserved in the mature region with only two nucleotides difference (Fig. 1C). Five Lsa-MIR396s were located on chromosome 1, 5, 7 and 8 respectively, among which chromosome 5 contained two Lsa-MIR396s, Lsa-MIR396a and Lsa-MIR396d (Fig. 1A). The identified GRF genes and miR396s in major species were listed and compared with those in lettuce (Table S1). The LsaGRF family was the second largest, and the number of miR396s was comparable to that in rice and tomato.

Table 1

Characteristics of the GRFs in lettuce
Name	Accession No.	Chr	CDS (bp)	Exon No.	Length (aa)	MW (KDa)	pI
LsaGRF1	Lsat_1_v5_gn_2_135541.1	Chr02	990	3	329	36.06	8.76
LsaGRF2	Lsat_1_v5_gn_3_14660.1	Chr03	1227	4	408	44.51	6.24
LsaGRF3	Lsat_1_v5_gn_3_85521.1	Chr03	999	4	332	37.74	8.73
LsaGRF4	Lsat_1_v5_gn_3_133500.1	Chr03	702	2	233	27.17	9.63
LsaGRF5	Lsat_1_v5_gn_4_92941.1	Chr04	951	3	316	36.58	8.81
LsaGRF6	Lsat_1_v5_gn_4_159961.1	Chr04	1551	4	516	56.20	7.70
LsaGRF7	Lsat_1_v5_gn_5_54781.3	Chr05	603	6	200	22.70	9.27
LsaGRF8	Lsat_1_v5_gn_5_141200.1	Chr05	990	3	329	37.54	8.24
LsaGRF9	Lsat_1_v5_gn_6_10680.1	Chr06	459	2	152	16.89	8.66
LsaGRF10	Lsat_1_v5_gn_6_17460.1	Chr06	897	3	298	33.12	6.44
LsaGRF11	Lsat_1_v5_gn_6_70601.1	Chr06	1113	4	370	40.08	8.23
LsaGRF12	Lsat_1_v5_gn_6_75441.1	Chr06	1014	3	337	37.60	8.74
LsaGRF13	Lsat_1_v5_gn_6_81681.1	Chr06	1029	4	342	36.78	7.09
LsaGRF14	Lsat_1_v5_gn_8_86361.1	Chr08	1071	3	356	40.63	8.97
LsaGRF15	Lsat_1_v5_gn_9_78540.1	Chr09	1233	4	410	44.10	7.67

Phylogenetic analysis, gene structures and motif divergence of LsaGRFs

To explore the evolutionary relationship of GRF gene family in different species, phylogenetic analysis on intron-exon and motif characteristics of LsaGRFs were performed. Phylogenetic analysis of GRF family in lettuce was firstly assessed and visualized using a Neighbor-Joining phylogenetic tree (Fig. 2A). All of the 15 LsaGRFs were divided into two groups (including 9 and 6 LsaGRFs respectively), each of which contained two small subgroups in the phylogenetic tree. Gene structure and motifs were considered to have a divergence during gene evolution. Therefore, the gene structures and motifs were listed in phylogenetic tree’s order (Fig. 2B). Most LsaGRF genes contain three or four exons. The LsaGRF genes containing the same number of exons were in the same group. For examples, LsaGRF4 and LsaGRF9 both have two exons. LsaGRF11, 1, 2 and 13 have four exons and the rests in another group have three exons expect LsaGRF7 (Fig. 2B). In conserved motifs analysis, motif 1 (yellow rectangle) and motif 2 (purple rectangle) were present to be the WRC and QLQ protein domain. As shown in Fig. 2B, the location of LsaGRF genes in phylogenetic tree were determined by the position and numbers of QLQ and WRC domains. All these analyses showed that the evolutionary relationship of LsaGRF genes was highly consistent with the gene structures and motif divergence of GRF genes in lettuce.

The functions of GRF genes in Arabidopsis and rice were extensively studied. The evolutionary relationship of GRF genes in lettuce, Arabidopsis and rice were helpful for putative function prediction of GRF genes in lettuce. There are totally 12 and 9 GRF genes in rice and Arabidopsis, respectively. The Neighbor-Joining phylogenetic tree of GRF genes from lettuce, rice and Arabidopsis showed that there were six groups according to the tree (Fig. 3). It was revealed that the evolutionary relationship of GRF genes in lettuce, rice and Arabidopsis were divergence. There were two groups, group I and VII, harboring GRF genes from lettuce, rice and Arabidopsis, which indicated that these LsaGRFs had putative orthologous genes in both rice and Arabidopsis. In group II and IV, there were just LsaGRFs and AtGRFs, but no GRF genes from rice, while there was no GRF gene from Arabidopsis in group VI. Group III contained only two LsaGRFs, LsaGRF4 and LsaGRF9, but no AtGRFs or OsGRFs, while group V contained three OsGRFs and one AtGRF gene, but no LsaGRF gene. These results probably suggested that the orthologous genes of some LsaGRFs had species specificity and some OsGRFs and AtGRFs had no ortholog in lettuce. Among the nine AtGRF genes, six GRF genes, AtGRF1, AtGRF2, AtGRF3, AtGRF4, AtGRF5 and AtGRF9, were proved to function in leaf development [3, 4, 12]. Interestingly, the role of AtGRF5 could not be taken over by other members of AtGRFs, though there were partly overlapping functions between AtGRFs [3, 12]. Therefore, we chose the putative homolog gene of AtGRF5, LsaGRF5, based on the evolutionary relationship derived from phylogenic tree for further functional analysis (Fig. 3).

Phylogenetic tree was constructed for 15 Lactuca sativa, 9 Arabidopsis thaliana and 12 Oryza sativa GRF proteins. There were 7 phylogenetic clusters designated as I–VII. LsaGRFs were written with red fronts. The cluster III that contained GRFs only from lettuce was highlighted with green and the cluster V without LsaGRFs was shaded in red. The LsaGRF5, which was selected for further investigation, were highlighted in yellow. The scale bar represents 0.1 amino acid changes per site.

Functional characterization of LsaGRF5

To characterize the putative functions of LsaGRF5, the expression profile of LsaGRF5 was detected. From the quantitative real-time PCR (qRT-PCR) results, the expression levels of LsaGRF5 in roots and leaves were relatively low, while those in the bud were significantly high (Fig. 4A). However, in mature flowers with mature pollens and pistils, the expression level of LsaGRF5 was much lower comparing that in the bud (Fig. 4A), indicating that LsaGRF5 probably function in flower development. Meanwhile, we also detected the expressions of Lsa-miR396a, putatively regulating the expression of GRF genes, in these tissues. We found that Lsa-miR396a were relatively highly expressed in stem, cotyledon and mature flower, while significantly much lower in buds (Fig. 4A). The tissues with high Lsa-miR396a expression, e.g. mature flowers and stems, showed relatively low expression of LsaGRF5. And vice versa the tissues with high LsaGRF5 expression, e.g. buds, showed relatively low expression of Lsa-miR396a., indicating that LsaGRF5 might be regulated by Lsa-miR396a.

The LsaGRF proteins are putative TFs. We chose the LsaGRF5 and performed its subcellular location observation and transactivation assay. We isolated the protoplast cell of lettuce and transformed the vector containing 35S:LsaGRF5-GFP and 35S:Ghd7-mCherry, which was reported to locate in nuclear, into lettuce protoplast cells. The empty vector was used for control. As shown in Fig. 4B, green fluorescence of GFP and red fluorescence of mCherry were totally overlapped in the protoplast cell transformed by 35S:LsaGRF5-GFP, indicating that the LsaGRF5-GFP and Ghd7-mCherry have the same nuclear localization. While the protoplast cell transformed by empty vector exhibited ubiquitous green fluorescence, excepting the overlapped region with the red nuclear fluorescence of Ghd7-mCherry (Fig. 4B). Therefore, LsaGRF5 located in the nucleus.

To identify which part of the LsaGRF5 protein had the transcriptional activity, we divided the LsaGRF5 into two parts based on the conserved protein domains. One part is the N-terminal of LsaGRF5, GRF5_{1 − 154}, containing QLQ and WRC domains, and the other, GRF5_{155 − 317} (Fig. 4C). Full-length and two partial LsaGRF5s were constructed into yeast expression vector, pGBD-T7. The empty vector pGBD-T7 and pGBD-T7-OsMYB103L which was proved to have transcriptional activity were designed as the negative and positive control, respectively [37]. These recombinant plasmids were transformed into yeast strain Y2HGold. They showed similar growth states without Tryptophan (Trp) under different diluted concentration (Fig. 4D), indicating that the recombinant plasmids were indeed transformed into the yeast cells and the transformation made few influences on the yeast growth. The yeast cells expressed full-length GRF5 and GRF5_{155 − 317} could grow with AbA (Aureobasidin A) and turn blue with X-α-galactoside, which were the same as the positive control (Fig. 4D). These results suggested that the C-terminal contributed to the transcriptional activity of LsaGRF5, while the N-terminal containing QLQ and WRC domains did not.

LsaGRF5 is a miR396a target gene in lettuce

The GRF gene family is known as the target of miR396 [21, 22]. To verify this in lettuce, we firstly predicted the complementarity between Lsa-miR396 and LsaGRFs. Lsa-miR396a shared nearly perfect complementarity with 14 LsaGRFs except LsaGRF9 (Fig. S3). The free energies of duplex structures were all lower than − 30 kcal/mol except for LsaGRF9 (-30.6 kcal/mol) (Fig. S3). It means that all LsaGRF genes except for LsaGRF9 probably were the targets of Lsa-miR396a. We chose LsaGRF5 for further verification, and performed the 5’ RNA ligase-mediated (RLM) rapid amplification of cDNA ends (RACE) assay. The results showed that the 1 ~ 10 bp of the target sequence in LsaGRF5 did not exist in the sequencing results, which means the transcript of LsaGRF5 was cleaved at base 10 of the miR396 target site (Fig. 5). Therefore, LsaGRF5 was probably the target of Lsa-miR396a. Function analysis in vivo could further clarify the regulatory relationship between LsaGRF5 and Lsa-miR396.

The phenotypes of LsaGRF5 and Lsa-miR396 overexpression lines

To investigate the function of LsaGRF5, we constructed the overexpression lines in lettuce. LsaGRF5 driven by CaMV 35S promoter was transformed into the lettuce cultivar of Romaine type ‘YIDALI’ (YDL). Eleven independent transgenic lines were obtained. Transformation verification was carried out through a pair of primers located on 35S promoter and LsaGRF5, respectively. The results showed that five out of eleven were positive transgenic lines with the same band as the positive control (Fig. 6A). qRT-PCR assay revealed that the expression of LsaGRF5 increased 5 ~ 15 folds in these five lines (Fig. 6B). Two lines, LsaGRF5-OE5 and LsaGRF5-OE11, with high LsaGRF5 expressions were used for further phenotypic analysis. The leaves of LsaGRF5-OE5 and LsaGRF5-OE11 were significantly bigger than these of YDL transformed by empty vector (Fig. 6C). The bigger leaves also existed in LsaGRF5 overexpressed in Arabidopsis (Fig. S4). From these results, LsaGRF5 could enhance the leaf growth, and this function was conserved in Arabidopsis.

To figure out the functional relevance between Lsa-miR396a and LsaGRF5, we also overexpressed Lsa-MIR396a in YDL. Three positive transgenic lines were obtained by PCR of genomic DNA (Fig. 6A). The transcriptional levels of Lsa-miR396a were about 8 ~ 15 times higher in overexpression lines compared with negative control (Fig. 6B). Two overexpression lines with high expression level of Lsa-miR396a showed smaller leaves, the opposite phenotype of LsaGRF5-OE (Fig. 6C). We detected the expression level of LsaGRF5 in Lsa-miR396-OE lines, and the results revealed that they were suppressed in Lsa-miR396a-OE lines (Fig. 6D). These results suggested that LsaGRF5 was an enhancer factor in leaf growth, while Lsa-miR396a was a repressor, and Lsa-miR396a regulated LsaGRF5 in functioning.

GROWTH-REGULATING FACTOR, a type of plant specific transcription factor, plays important roles in plant growth and development. Therefore, genome organization and function of GRF family members were evaluated in various plant species. Our studies focus on the genome organization, conservation and function of GRFs in lettuce. Thus, we identified 15 GRF genes based on the recently released genome data of lettuce cultivar ‘Salinas’ [36]. The regulatory genes are considered to be preferentially retained after genome duplications [38]. The GRF gene family has subjected to two expansions with one occurred through the whole-genome triplication in the common ancestor of eudicots and the other one occurred during independent whole-genome duplications in various plants [8]. Therefore, the GRF gene family shows distinct number of members in different species (Table S1). The number of GRF genes in lettuce (15 LsaGRFs) was nearly twice larger than that in Arabidopsis thalina (9 AtGRFs), suggesting that the GRF genes in lettuce may have experienced another independent expansion after the split of the Brassicaceae and the Compositae. Among the 15 identified LsaGRFs, not all LsaGRF genes contained both QLQ and WRC domains. LsaGRF7 contains only WRC domain, and LsaGRF4 contains two WRC domains but no QLQ domain, which might be the results from whole-genome duplication and recombination, and might play distinct roles in plant growth regulation (Fig. 2B). Interestingly, LsaGRF9, like rice and maize GRF10, had truncated C-terminal (Fig. 2B). Overexpression of ZmGRF10 may break the homeostasis of GRF/GIF (GRF INTERACTION FACTOR) to affect leaf growth, whether or not LsaGRF9 functioned in the same way needs to be further addressed.

LsaGRF5 was closest to AtGRF5 in evolutionary relationship (Fig. 3). AtGRF5 enhances cell proliferation but not cell expansion in the leaf. Overexpression of LsaGRF5 results in larger leaves in both lettuce and Arabidopsis thalina (Fig. 6C, Fig. S4) but whether it had the same regulatory mechanism with AtGRF5 during the leaf growth needs to be further explored. Through subcellular location and transactivation assay, LsaGRF5 probably worked as transcriptional factor in cell nucleus. Notably, AtGRF5 was proved to be able to interact with GIF1 to regulate cell proliferation in leaf primordium [3]. In addition, GIF proteins have recently been reported to play a role in transcription regulation not only by the interactions with GRFs but also with various chromatin remodeling proteins [12, 39]. Whether there were functional GIF genes in lettuce, and if LsaGRF5 could interact with GIF to regulate leaf growth needs further investigation. It is already known that miR396 directly cleaves the GRF genes on their complementary sequence to suppress their expression [22]. In this study, we firstly predicted that there were 14 GRF genes, except for LsaGRF9, as the putative targets of Lsa-miR396 based on the free energies of duplex structures analysis. The cleavage sites of LsaGRF5 were confirmed by 5’ RACE in vivo. At the same time, the expression of LsaGRF5 was significantly decreased in Lsa-miR396a-OE lines. Among nine GRF genes in Arabidopsis, AtGRF5 and AtGRF6 were found not to be the target of miR396 [21, 22]. AtGRF5, AtGRF6 and LsaGRF5 belonged to group VII, while LsaGRF9 was in group III (Fig. 3), suggesting that the regulation pattern of miR396-GRFs might be distinct in lettuce and Arabidopsis thalina. Recently, AtGRF5 was found to function in chloroplast development, nitrogen signaling and senescence, besides leaf development [40]. Therefore, besides some conserved function characteristic of GRF genes, it is valuable to know whether LsaGRF5 has other functions.

Expression profile of genes would help us to predict their potential biological function. The expression patterns of GRFs have been previously investigated. They usually express in growing zones of roots and shoots where cell proliferation occurs [2, 3, 10, 11, 13, 15]. Here, we detected the expression of LsaGRF5 in root, stem, cotyledon, leaf, bud and mature flower, and revealed that LsaGRF5 was highly expressed in bud where cell proliferation occurs violently. Moreover, expression level of AtGRF is suppressed during plant aging [2, 22]. The expression of LsaGRF5 in bud was significantly higher than that in mature flower, which is consistent with previous results that GRFs functioned in the early stages of the growth and development in different tissues [2, 3, 22].

In this study, we firstly identified all of the GRF gene family members in lettuce. The phylogenic relationship of these GRF genes in lettuce with their counterparts in Arabidopsis thalina and rice and conserved motif were evaluated. GRFs were well-known as target genes of miR396s. Therefore, thus is a daily use, we also characterized the chromosomal location of the stem-loop sequences features of Lsa-miR396s. Furthermore, LsaGRF5 could probably function as a transcriptional factor in cell nucleus through subcellular location observation and transactivation assay. Overexpression of LsaGRF5 could stimulate the leaf growth leading to bigger leaves, while overexpression of Lsa-miR396a exhibited smaller leaves with suppressed expression of LsaGRF5. In summary, the expression of LsaGRF5 was regulated by Lsa-miR396 through the cleavage of complementary sequences to control leaf growth. Our findings will facilitate further understanding of the functions of GRF genes and help elucidating the leaf development mechanism in lettuce.

Plant materials and growth conditions

The lettuce (Lactuca sativa L.) cultivar of Romaine type, cv. ‘YIDALI’ (YDL), was used for transformation in this study. The lettuce seeds were provided by Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China. The sterilized lettuce seeds were grown on Murashige and Skoog (MS) medium plus 3% sucrose and 0.6% agar (pH 5.8) at 25°C in a 16-h-light /8-h-dark cycle. The full expanded cotyledons were used for transformation. The transgenic lettuce plants were grown in a growth chamber under a photoperiod of 16-h light (200 μmol m^-2 s^-1) and 8-h dark at 25°C. When the fifth true leaf was fully expanded, the lettuce plants were transplanted into a greenhouse in Beijing Vegetable Research Center under standard greenhouse conditions.

2.2 Identification of GRF genes in lettuce

The genome sequences of lettuce (Lactuca sativa V8) were downloaded from the Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html). The sequences of Lsa-miR396s were obtained from PmiREN (Plant miRNA Encyclopedia, http://www.pmiren.com) [41]. The sequences of AtGRFs and OsGRFs were retrieved from the Arabidopsis thalina Information Resource (http://www.arabidopsis.org/) and China Rice Data Centre (http://www.ricedata.cn/) respectively. The amino acid and nucleotide sequences of AtGRFs and OsGRFs were used for BLASTp and BLASTn (E < 0.01) searching in Phytozome (Lactuca sativa V8) to obtain a list of putative LsaGRF genes. Subsequently, the amino acid sequences of the obtained putative LsaGRFs were reiteratively used for BLAST searching. The conserved protein domains in the GRF proteins, including QLQ (PF08880) and WRC (PF08879), were used for searching in the lettuce Protein Database in GRAMENE [42], and the protein domains of LsaGRFs were confirmed in the Pfam database (http://pfam.sanger.ac.uk/)(E-value < 1 × 10⁻⁴) [43]. Finally, the results were supplemented using the HMMER software.

2.3 Characterization of LsaGRFs and miR396s

The molecular masses of the putative GRF proteins were calculated using the Compute pI/Mw tool of ExPaSy (http://web.expasy.org/compute_pi/). Schematic LsaGRF gene structure diagrams were drawn using the Gene Structure Display Server (http://gsds.cbi.pku.edu.cn/). Protein sequence motifs were predicted using the MEME program (http://meme.sdsc.edu/meme/). The physical position of each LsaGRF gene on the ten Chinese cabbage chromosomes was determined from the Chinese cabbage database (BRAD, http://Chinesecabbagedb.org/brad/) and marked on each chromosome using the MapInspect software (http://mapinspect.software.informer.com). The combination of phylogenetic tree, gene, and protein structures was generated using the iTOL tool (http://itol.embl.de) [44].

Phylogenetic analysis

To construct the phylogeny of the GRFs from various species, multiple sequence alignments for all GRF amino acid sequences were conducted using MEGA 7.0 with default settings [45]. Phylogenetic analyses were carried out with a Neighbor-Joining method using MEGA 7.0 [45].

Lettuce protoplast isolation and subcellular location of LsaGRF5

The coding sequence of LsaGRF5 was cloned into the pSAT6-EGFP-N1 vector. The 35S:LsaGRF5-GFP and 35S:GFP plasmids were transformed into protoplasts of the lettuce ‘YDL’ by means of polyethylene glycol treatment [46]. Transformed protoplasts were observed using a ﬂuorescence microscope (Leica TCS SP5). Images were analyzed with Image LAS-AF software. Ghd7-mCherry was used as controls for nuclear [47]. Primers used were listed in Table S2.

Transactivation assay based on the yeast GAL4 system

The transcriptional activity of LsaGRF5 was evaluated in yeast cells. The full-length coding sequence, N-terminal LsaGRF5 DNA-binding domain (1–154 aa) and the C-terminal putative activation domain (155–317 aa) were (respectively) cloned into pBD-GAL4vector. The empty vectors pGBKT7 and GAL4 were used as negative and positive controls, respectively. All of these constructs were individually introduced into cells of yeast strain Y2HGold containing the AUR1-C and MEL1 reporter genes. Yeast cell transformation was carried out using the instructions in the Yeast maker^TM Yeast Transformation System 2 User Manual. The yeast transformants were grown on SD/-Trp and SD/-Trp/ in the presence of Aba and X-α-gal plates for 2–4 d at 30°C to identify transactivation activity (Yeast Protocols Handbook; Clontech, Mountain View, CA, USA). Primers used were showed in Table S2.

RNA extraction and qRT-PCR

Total RNA was extracted from the leaves using a plant RNeasy kit (Tiangen, Beijing, China). RNA was reverse transcribed into cDNA with a PrimeScript™ RT reagent Kit (Takara, Osaka, Japan). Real-time PCR reactions were performed using the SYBR Green I Master Mix and were quantified in a Light Cycler 480 II instrument (Roche, Basel, Switzerland). The PCR program comprised an initial step at 94 °C for 30 s, followed by 40 cycles of 94 °C for 10 s and 58 °C for 30 s. Amplification was followed by heating for 1 min at 60–95 °C for melting curve analysis. Each reaction was performed with three replications using 5 µL of Master Mix, 0.25 µM of each primer, 1 µL of diluted cDNA, and DNase-free water to a final volume of 10 µL. According to Yu et al. 2020 [48], the lettuce actin genes were used as internal controls to normalize the transcript levels of target genes. Relative gene quantification was calculated by the comparative ΔΔCt method [49]. The average 2−ΔΔCt values were used to determine differences in gene transcript levels. The lengths of PCR products were among 300 to 500 bp. The PCR products were sequenced in a commercial DNA sequencing company. The primers were designed using the Primer Premier 6.0 software and were shown in Table S2.

Plasmid construction and plant transformation

The cloning primers of LsaGRF5 and Lsa-MIR396a were designed based on the genome sequences of lettuce (Lactuca sativa V8) from the Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html). The coding sequences of LsaGRF5 and Lsa-MIR396a were cloned from the lettuce ‘YDL’ and constructed into the overexpression vector pEZR(K)-LC driven by 35S promoter using 2 X Seamless Cloning Mix (Biomed, CL117-01, Beijing). The primers used for vector construction were listed in Table S2.

MiR396 cleavage site analysis

A 5’ RLM-RACE was used to detect the miR396 cleavage site in miR396 target genes and was performed accordingly [50]. The gene-speciﬁc primers (GSPs) and 5’adaptor sequences were listed in Table S2. The target DNA fragment was puriﬁed and cloned into vector using pEASY-Blunt Zero Cloning Kit (TransGene, CB501-01, Beijing, China). At least 15 positive clones of each gene were picked for sequencing.

MW: Molecular weight

GRFs: GROWTH-REGULATING FACTORs

GA: gibberellic acid

TF: transcription factor

SAM: shoot apical meristems

Ad-Ab: adaxial–abaxial

GIF: GRF-Interacting Factors

AbA: Aureobasidin A

MS: Murashige and Skoog

pI: Isoelectric point

qRT–PCR: Quantitative real-time polymerase chain reaction

5’ RLM RACE assay: 5’ RNA ligase-mediated rapid ampliﬁcation of cDNA ends assay

Acknowledgements

We would like to thank Dr. Maoyin Li for his critical reading on the manuscript.

Funding

This work was supported by grants from the Beijing Vegetable Research Center [KYCX202002-01 and KYCX201901-01], the Beijing Academy of Agriculture and Forestry Science [KJCX20200113].

Availability of data and materials

The genome and protein sequences of LsaGRFs (Lactuca sativa V8) were downloaded from the Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html). The sequences of Lsa-miR396s were obtained from PmiREN (Plant miRNA Encyclopedia, http://www.pmiren.com). All of the datasets supporting the results of this article are included within the article and its additional files. The sequences of AtGRFs and OsGRFs were retrieved from the Arabidopsis thalina Information Resource (http://www.arabidopsis.org/) and China Rice Data Centre (http://www.ricedata.cn/) respectively.

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests

Authors’ Contributions

D.L, D. Z., and B. Z. designed experiments. B. Z., Y. T. and D. Z. identified and characterized the GRF genes family in lettuce. B. Z., Y. T., K. L., Z.Z., and X.L. carried out the experiment. B.Z., and D. L. wrote the paper. All authors discussed the results and commented on the manuscript.

van der Knaap E, Kim JH, Kende H: A novel gibberellin-induced gene from rice and its potential regulatory role in stem growth. Plant physiology 2000, 122(3):695-704.
Kim JH, Choi D, Kende H: The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis. The Plant Journal 2003, 36(1):94-104.
Horiguchi G, Kim G-T, Tsukaya H: The transcription factor AtGRF5 and the transcription coactivator AN3 regulate cell proliferation in leaf primordia of Arabidopsis thaliana. The Plant Journal 2005, 43(1):68-78.
Kim JH, Lee BH: GROWTH-REGULATING FACTOR4 ofArabidopsis thaliana is required for development of leaves, cotyledons, and shoot apical meristem. Journal of Plant Biology 2006, 49(6):463-468.
Powell Anahid E, Lenhard M: Control of Organ Size in Plants. Current Biology 2012, 22(9):R360-R367.
Hepworth J, Lenhard M: Regulation of plant lateral-organ growth by modulating cell number and size. Current Opinion in Plant Biology 2014, 17:36-42.
Kim JH, Tsukaya H: Regulation of plant growth and development by the GROWTH-REGULATING FACTOR and GRF-INTERACTING FACTOR duo. Journal of Experimental Botany 2015, 66(20):6093-6107.
Omidbakhshfard Mohammad A, Proost S, Fujikura U, Mueller-Roeber B: Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology. Molecular Plant 2015, 8(7):998-1010.
Hewezi T, Maier TR, Nettleton D, Baum TJ: The Arabidopsis MicroRNA396-GRF1/GRF3 Regulatory Module Acts as a Developmental Regulator in the Reprogramming of Root Cells during Cyst Nematode Infection. Plant Physiology 2012, 159(1):321.
Kim J-S, Mizoi J, Kidokoro S, Maruyama K, Nakajima J, Nakashima K, Mitsuda N, Takiguchi Y, Ohme-Takagi M, Kondou Y et al: Arabidopsis growth-regulating factor7 functions as a transcriptional repressor of abscisic acid- and osmotic stress-responsive genes, including DREB2A. Plant Cell 2012, 24(8):3393-3405.
Bao M, Bian H, Zha Y, Li F, Sun Y, Bai B, Chen Z, Wang J, Zhu M, Han N: miR396a-Mediated Basic Helix–Loop–Helix Transcription Factor bHLH74 Repression Acts as a Regulator for Root Growth in Arabidopsis Seedlings. Plant and Cell Physiology 2014, 55(7):1343-1353.
Debernardi JM, Mecchia MA, Vercruyssen L, Smaczniak C, Kaufmann K, Inze D, Rodriguez RE, Palatnik JF: Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity. The Plant Journal 2014, 79(3):413-426.
Liang G, He H, Li Y, Wang F, Yu D: Molecular Mechanism of microRNA396 Mediating Pistil Development in Arabidopsis. Plant Physiology 2014, 164(1):249.
Liu H, Guo S, Xu Y, Li C, Zhang Z, Zhang D, Xu S, Zhang C, Chong K: OsmiR396d-Regulated OsGRFs Function in Floral Organogenesis in Rice through Binding to Their Targets OsJMJ706 and OsCR4</em&gt. Plant Physiology 2014, 165(1):160.
Pajoro A, Madrigal P, Muiño JM, Matus JT, Jin J, Mecchia MA, Debernardi JM, Palatnik JF, Balazadeh S, Arif M et al: Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development. Genome biology 2014, 15(3):R41-R41.
Choi D, Kim JH, Kende H: Whole Genome Analysis of the OsGRF Gene Family Encoding Plant-Specific Putative Transcription Activators in Rice (Oryza sativa L.). Plant and Cell Physiology 2004, 45(7):897-904.
Treich I, Cairns BR, de los Santos T, Brewster E, Carlson M: SNF11, a new component of the yeast SNF-SWI complex that interacts with a conserved region of SNF2. Molecular and Cellular Biology 1995, 15(8):4240.
Raventós D, Skriver K, Schlein M, Karnahl K, Rogers SW, Rogers JC, Mundy J: HRT, a Novel Zinc Finger, Transcriptional Repressor from Barley*. Journal of Biological Chemistry 1998, 273(36):23313-23320.
Debernardi JM, Rodriguez RE, Mecchia MA, Palatnik JF: Functional specialization of the plant miR396 regulatory network through distinct microRNA-target interactions. PLoS Genet 2012, 8(1):e1002419-e1002419.
Arvidsson S, Pérez-Rodríguez P, Mueller-Roeber B: A growth phenotyping pipeline for Arabidopsis thaliana integrating image analysis and rosette area modeling for robust quantification of genotype effects. New Phytologist 2011, 191(3):895-907.
Liu D, Song Y, Chen Z, Yu D: Ectopic expression of miR396 suppresses GRF target gene expression and alters leaf growth in Arabidopsis. Physiologia Plantarum 2009, 136(2):223-236.
Rodriguez RE, Mecchia MA, Debernardi JM, Schommer C, Weigel D, Palatnik JF: Control of cell proliferation in Arabidopsis thaliana by microRNA miR396. Development 2010, 137(1):103.
Wang L, Gu X, Xu D, Wang W, Wang H, Zeng M, Chang Z, Huang H, Cui X: miR396-targeted AtGRF transcription factors are required for coordination of cell division and differentiation during leaf development in Arabidopsis. Journal of experimental botany 2011, 62(2):761-773.
Liu J, Hua W, Yang H-L, Zhan G-M, Li R-J, Deng L-B, Wang X-F, Liu G-H, Wang H-Z: The BnGRF2 gene (GRF2-like gene from Brassica napus) enhances seed oil production through regulating cell number and plant photosynthesis. Journal of experimental botany 2012, 63(10):3727-3740.
Hu J, Wang Y, Fang Y, Zeng L, Xu J, Yu H, Shi Z, Pan J, Zhang D, Kang S et al: A Rare Allele of GS2 Enhances Grain Size and Grain Yield in Rice. Molecular Plant 2015, 8(10):1455-1465.
Sun P, Zhang W, Wang Y, He Q, Shu F, Liu H, Wang J, Wang J, Yuan L, Deng H: OsGRF4 controls grain shape, panicle length and seed shattering in rice. Journal of Integrative Plant Biology 2016, 58(10):836-847.
Kim JH: Biological roles and an evolutionary sketch of the GRF-GIF transcriptional complex in plants. BMB Rep 2019, 52(4):227-238.
Luo G, Palmgren M: GRF-GIF Chimeras Boost Plant Regeneration. Trends in Plant Science 2020.
Zhang D-F, Li B, Jia G-Q, Zhang T-F, Dai J-R, Li J-S, Wang S-C: Isolation and characterization of genes encoding GRF transcription factors and GIF transcriptional coactivators in Maize (Zea mays L.). Plant Science 2008, 175(6):809-817.
Wang F, Qiu N, Ding Q, Li J, Zhang Y, Li H, Gao J: Genome-wide identification and analysis of the growth-regulating factor family in Chinese cabbage (Brassica rapa L. ssp. pekinensis). BMC Genomics 2014, 15(1):807-807.
Cao D, Wang J, Ju Z, Liu Q, Li S, Tian H, Fu D, Zhu H, Luo Y, Zhu B: Regulations on growth and development in tomato cotyledon, flower and fruit via destruction of miR396 with short tandem target mimic. Plant Science 2016, 247:1-12.
Cao Y, Han Y, Jin Q, Lin Y, Cai Y: Comparative Genomic Analysis of the GRF Genes in Chinese Pear (Pyrus bretschneideri Rehd), Poplar (Populous), Grape (Vitis vinifera), Arabidopsis and Rice (Oryza sativa). Front Plant Sci 2016, 7:1750-1750.
Ma J-Q, Jian H-J, Yang B, Lu K, Zhang A-X, Liu P, Li J-N: Genome-wide analysis and expression profiling of the GRF gene family in oilseed rape (Brassica napus L.). Gene 2017, 620:36-45.
Zhang J, Li Z, Jin J, Xie X, Zhang H, Chen Q, Luo Z, Yang J: Genome-wide identification and analysis of the growth-regulating factor family in tobacco (Nicotiana tabacum). Gene 2018, 639:117-127.
Wang J, Zhou H, Zhao Y, Sun P, Tang F, Song X, Lu M-Z: Characterization of poplar growth-regulating factors and analysis of their function in leaf size control. BMC Plant Biol 2020, 20(1):509-509.
Reyes-Chin-Wo S, Wang Z, Yang X, Kozik A, Arikit S, Song C, Xia L, Froenicke L, Lavelle DO, Truco M-J et al: Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat Commun 2017, 8:14953-14953.
Yang C, Li D, Liu X, Ji C, Hao L, Zhao X, Li X, Chen C, Cheng Z, Zhu L: OsMYB103L, an R2R3-MYB transcription factor, influences leaf rolling and mechanical strength in rice (Oryza sativa L.). BMC Plant Biol 2014, 14:158-158.
Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y: Modeling gene and genome duplications in eukaryotes. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(15):5454.
Vercruyssen L, Verkest A, Gonzalez N, Heyndrickx KS, Eeckhout D, Han S-K, Jégu T, Archacki R, Van Leene J, Andriankaja M et al: ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development. Plant Cell 2014, 26(1):210-229.
Vercruyssen L, Tognetti VB, Gonzalez N, Van Dingenen J, De Milde L, Bielach A, De Rycke R, Van Breusegem F, Inzé D: GROWTH REGULATING FACTOR5 Stimulates Arabidopsis Chloroplast Division, Photosynthesis, and Leaf Longevity. Plant Physiology 2015, 167(3):817.
Guo Z, Kuang Z, Wang Y, Zhao Y, Tao Y, Cheng C, Yang J, Lu X, Hao C, Wang T et al: PmiREN: a comprehensive encyclopedia of plant miRNAs. Nucleic Acids Res 2020, 48(D1):D1114-D1121.
Ware DH, Jaiswal P, Ni J, Yap IV, Pan X, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K et al: Gramene, a Tool for Grass Genomics. Plant Physiology 2002, 130(4):1606.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J et al: The Pfam protein families database. Nucleic Acids Res 2012, 40(Database issue):D290-D301.
Letunic I, Bork P: Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 2011, 39(Web Server issue):W475-W478.
Kumar S, Stecher G, Tamura K: MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular Biology and Evolution 2016, 33(7):1870-1874.
Yoo S-D, Cho Y-H, Sheen J: Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nature Protocols 2007, 2(7):1565-1572.
Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X et al: Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nature Genetics 2008, 40(6):761-767.
Yu C, Yan C, Liu Y, Liu Y, Jia Y, Lavelle D, An G, Zhang W, Zhang L, Han R et al: Upregulation of a KN1 homolog by transposon insertion promotes leafy head development in lettuce. Proceedings of the National Academy of Sciences 2020, 117(52):33668.
Schmittgen TD, Livak KJ: Analyzing real-time PCR data by the comparative CT method. Nature Protocols 2008, 3(6):1101-1108.
Wang C, Fang J: RLM-RACE, PPM-RACE, and qRT-PCR: An Integrated Strategy to Accurately Validate miRNA Target Genes. In: Small Non-Coding RNAs: Methods and Protocols. Edited by Rederstorff M. New York, NY: Springer New York; 2015: 175-186.

No competing interests reported.

additionalfile1.docx
Additional file 1：Supplemental figures Figure S1. The amino acid sequences alignment of LsaGRF genes. Figure S2. Phylogenetic analysis of Lsa-miR396s. Figure S3. The degree of Lsa-miR396a complementarity to all LsaGRFs. Figure S4. The phenotypes of overexpression lines of LsaGRF5 in Arabidopsis.
additionalfile2.xlsx
Additional file 2：Table S1 Number of GRF genes and miR396s have been identified in different species
additionalfile3.xlsx
Additional file 3：Table S2 The sequences of Primers used in this study

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Identification of GROWTH-REGULATING FACTOR Transcription Factor Family Involved in Leaf Growth Regulation in Lettuce (Lactuca sativa L.)

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Version 1

Abstract

Figures

Introduction

Results

Identification of the GRF genes and miR396s in lettuce

Phylogenetic analysis, gene structures and motif divergence of LsaGRFs

Functional characterization of LsaGRF5

LsaGRF5 is a miR396a target gene in lettuce

The phenotypes of LsaGRF5 and Lsa-miR396 overexpression lines

Discussion

Materials And Methods

Plant materials and growth conditions

2.2 Identification of GRF genes in lettuce

2.3 Characterization of LsaGRFs and miR396s

Phylogenetic analysis

Lettuce protoplast isolation and subcellular location of LsaGRF5

Transactivation assay based on the yeast GAL4 system

RNA extraction and qRT-PCR

Plasmid construction and plant transformation

MiR396 cleavage site analysis

Abbreviations

Declarations

Acknowledgements

Funding

Availability of data and materials

Ethics approval and consent to participate

Consent for publication

Competing interests

Authors’ Contributions

References

Additional Declarations

Supplementary Files

Status:

Version 1