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Genome-wide characterization, expression and functional analysis of CLV3/ESR gene family in tomato.

Zhang Y, Yang S, Song Y, Wang J - BMC Genomics (2014)

Bottom Line: In particular, SlCLE12, the homologue of Arabidopsis CLE41/44 gene, appears to be the dominant CLE gene in most of tested tissues with its maximum expression found in vascular tissues.Upon the treatment with synthetic peptides corresponding to the 12-aa CLE domains of SlCLE 10, 12 and 13, tomato seedlings exhibit a clear reduction in root length to varying degrees.Differential expression patterns of various SlCLEs provide important insights into the functional divergence of CLE signaling cascade in Solanaceae species, especially their potential involvements in the regulation of fruit development and ripening.

View Article: PubMed Central - PubMed

Affiliation: School of Environmental Science and Engineering, Tianjin University, Weijin Rd, 92#, Nankai District, Tianjin 300072, China. jiehuawang@tju.edu.cn.

ABSTRACT

Background: By encoding a group of small secretory peptides, the members of the CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) family play important roles in cell-to-cell communication to control the balance between stem cell proliferation and differentiation in plant development. Despite recent identification and characterization of members of this gene family in several plant species, little is known about its functional role in plants with fleshy fruits.

Results: In total, fifteen CLE genes (SlCLE1-15) were identified from tomato (Solanum lycopersicum cv. 'Heinz-1706') genome and their multiple characters including phylogeny, gene structures, chromosome locations, conserved motifs and cis-elements in the promoter sequences, were analyzed. Real-time PCR analysis showed that 13 out of 15 identified SlCLE genes are transcribed and exhibit remarkably unique expression patterns among tissues and organs. In particular, SlCLE12, the homologue of Arabidopsis CLE41/44 gene, appears to be the dominant CLE gene in most of tested tissues with its maximum expression found in vascular tissues. Meanwhile, SlCLE1, 10, 13 exhibit specific but distinct expression in flower bud, root and shoot apex, respectively. More notably, several SlCLEs are dramatically regulated in their transcriptional levels during fruit development and ripening, indicating significant role these genes may potentially play in the critical physiological process. Upon the treatment with synthetic peptides corresponding to the 12-aa CLE domains of SlCLE 10, 12 and 13, tomato seedlings exhibit a clear reduction in root length to varying degrees.

Conclusions: This study provides a comprehensive genomic analysis of CLE gene family in tomato, a crop species with fleshy fruit. Differential expression patterns of various SlCLEs provide important insights into the functional divergence of CLE signaling cascade in Solanaceae species, especially their potential involvements in the regulation of fruit development and ripening.

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Phylogenetic tree and sequence analysis of tomato andArabidopsis CLEgene families. (A) Maximum likelihood bootstrap tree phylogeny based on the CLE motif sequences of SlCLE genes in tomato. The unrooted tree was constructed using MEGA 5.05. Numbers at nodes indicate the percentage bootstrap scores and only bootstrap values higher than 40% from 1,000 replicates are shown. Sl, S. lycopersicum; At, A. thaliana; Zm, Z. Maize. (B) Predicted protein sequences of SlCLEs were aligned with AtCLEs with flanking sequences using ClustalX and the output was displayed with Box Shade. (C) Sequence logos for the CLE motifs of tomato and Arabidopsis CLE gene family members. The height of the bars indicates the number of identical residues per position.
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Fig1: Phylogenetic tree and sequence analysis of tomato andArabidopsis CLEgene families. (A) Maximum likelihood bootstrap tree phylogeny based on the CLE motif sequences of SlCLE genes in tomato. The unrooted tree was constructed using MEGA 5.05. Numbers at nodes indicate the percentage bootstrap scores and only bootstrap values higher than 40% from 1,000 replicates are shown. Sl, S. lycopersicum; At, A. thaliana; Zm, Z. Maize. (B) Predicted protein sequences of SlCLEs were aligned with AtCLEs with flanking sequences using ClustalX and the output was displayed with Box Shade. (C) Sequence logos for the CLE motifs of tomato and Arabidopsis CLE gene family members. The height of the bars indicates the number of identical residues per position.

Mentions: We then examined the phylogenetic relationship of the putative SlCLE family members to Arabidopsis CLEs and certain well-known CLE proteins from other species. Because the majority of SlCLE family members have very divergent amino acid sequences outside the CLE motifs, their phylogenetic relationship was not well supported (FigureĀ 1A). However, some branches in the tree were supported by high bootstrap values and thus indicated the most closely related CLE proteins. We are confident of the close relationship of SlCLE15 (Solyc11g071380) to FLORAL ORGAN NUMBER2 and 4 (OsFON2/FON4), which have been reported to regulate floral meristem size in rice[22, 23]. SlCLE10 (Solyc07g053370) and SlCLE11 (Solyc07g062670) are clustered together with AtCLE1-7, which genes form a single subclade among Arabidopsis 32 CLE members. The overexpression of AtCLE1-7 is known to cause a premature termination of SAM and longer roots as well[24, 25]. Interestingly, the functional forms of the above-mentioned three SlCLEs (SlCLE15, SlCLE10 and SlCLE11) are also the SlCLEs sharing the highest sequence similarity with the well-known AtCLV3 and ZmESR1-3. CLV3 encodes a stem cell-specific protein that plays a key role in stem cell fate determination through mediating the intercellular communication during Arabidopsis development[26, 27]. ZmESRs are endosperm-specific genes in maize and are supposed to play roles in the nutrition of the developing embryo and in the establishment of a physical barrier between embryo and endosperm[28]. When compared to the 26 predicted active CLE peptides encoded by Arabidopsis CLE genes, a perfect match in tomato was only found for SLCLE12 (Solyc09g061410) with the TDIF peptide encoded by AtCLE41/44. TDIF plays a specific role in xylem differentiation[2] and very recently, its perfect conservation in amino acid sequences has been reported across eight conifer species[29] .Figure 1


Genome-wide characterization, expression and functional analysis of CLV3/ESR gene family in tomato.

Zhang Y, Yang S, Song Y, Wang J - BMC Genomics (2014)

Phylogenetic tree and sequence analysis of tomato andArabidopsis CLEgene families. (A) Maximum likelihood bootstrap tree phylogeny based on the CLE motif sequences of SlCLE genes in tomato. The unrooted tree was constructed using MEGA 5.05. Numbers at nodes indicate the percentage bootstrap scores and only bootstrap values higher than 40% from 1,000 replicates are shown. Sl, S. lycopersicum; At, A. thaliana; Zm, Z. Maize. (B) Predicted protein sequences of SlCLEs were aligned with AtCLEs with flanking sequences using ClustalX and the output was displayed with Box Shade. (C) Sequence logos for the CLE motifs of tomato and Arabidopsis CLE gene family members. The height of the bars indicates the number of identical residues per position.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4195864&req=5

Fig1: Phylogenetic tree and sequence analysis of tomato andArabidopsis CLEgene families. (A) Maximum likelihood bootstrap tree phylogeny based on the CLE motif sequences of SlCLE genes in tomato. The unrooted tree was constructed using MEGA 5.05. Numbers at nodes indicate the percentage bootstrap scores and only bootstrap values higher than 40% from 1,000 replicates are shown. Sl, S. lycopersicum; At, A. thaliana; Zm, Z. Maize. (B) Predicted protein sequences of SlCLEs were aligned with AtCLEs with flanking sequences using ClustalX and the output was displayed with Box Shade. (C) Sequence logos for the CLE motifs of tomato and Arabidopsis CLE gene family members. The height of the bars indicates the number of identical residues per position.
Mentions: We then examined the phylogenetic relationship of the putative SlCLE family members to Arabidopsis CLEs and certain well-known CLE proteins from other species. Because the majority of SlCLE family members have very divergent amino acid sequences outside the CLE motifs, their phylogenetic relationship was not well supported (FigureĀ 1A). However, some branches in the tree were supported by high bootstrap values and thus indicated the most closely related CLE proteins. We are confident of the close relationship of SlCLE15 (Solyc11g071380) to FLORAL ORGAN NUMBER2 and 4 (OsFON2/FON4), which have been reported to regulate floral meristem size in rice[22, 23]. SlCLE10 (Solyc07g053370) and SlCLE11 (Solyc07g062670) are clustered together with AtCLE1-7, which genes form a single subclade among Arabidopsis 32 CLE members. The overexpression of AtCLE1-7 is known to cause a premature termination of SAM and longer roots as well[24, 25]. Interestingly, the functional forms of the above-mentioned three SlCLEs (SlCLE15, SlCLE10 and SlCLE11) are also the SlCLEs sharing the highest sequence similarity with the well-known AtCLV3 and ZmESR1-3. CLV3 encodes a stem cell-specific protein that plays a key role in stem cell fate determination through mediating the intercellular communication during Arabidopsis development[26, 27]. ZmESRs are endosperm-specific genes in maize and are supposed to play roles in the nutrition of the developing embryo and in the establishment of a physical barrier between embryo and endosperm[28]. When compared to the 26 predicted active CLE peptides encoded by Arabidopsis CLE genes, a perfect match in tomato was only found for SLCLE12 (Solyc09g061410) with the TDIF peptide encoded by AtCLE41/44. TDIF plays a specific role in xylem differentiation[2] and very recently, its perfect conservation in amino acid sequences has been reported across eight conifer species[29] .Figure 1

Bottom Line: In particular, SlCLE12, the homologue of Arabidopsis CLE41/44 gene, appears to be the dominant CLE gene in most of tested tissues with its maximum expression found in vascular tissues.Upon the treatment with synthetic peptides corresponding to the 12-aa CLE domains of SlCLE 10, 12 and 13, tomato seedlings exhibit a clear reduction in root length to varying degrees.Differential expression patterns of various SlCLEs provide important insights into the functional divergence of CLE signaling cascade in Solanaceae species, especially their potential involvements in the regulation of fruit development and ripening.

View Article: PubMed Central - PubMed

Affiliation: School of Environmental Science and Engineering, Tianjin University, Weijin Rd, 92#, Nankai District, Tianjin 300072, China. jiehuawang@tju.edu.cn.

ABSTRACT

Background: By encoding a group of small secretory peptides, the members of the CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) family play important roles in cell-to-cell communication to control the balance between stem cell proliferation and differentiation in plant development. Despite recent identification and characterization of members of this gene family in several plant species, little is known about its functional role in plants with fleshy fruits.

Results: In total, fifteen CLE genes (SlCLE1-15) were identified from tomato (Solanum lycopersicum cv. 'Heinz-1706') genome and their multiple characters including phylogeny, gene structures, chromosome locations, conserved motifs and cis-elements in the promoter sequences, were analyzed. Real-time PCR analysis showed that 13 out of 15 identified SlCLE genes are transcribed and exhibit remarkably unique expression patterns among tissues and organs. In particular, SlCLE12, the homologue of Arabidopsis CLE41/44 gene, appears to be the dominant CLE gene in most of tested tissues with its maximum expression found in vascular tissues. Meanwhile, SlCLE1, 10, 13 exhibit specific but distinct expression in flower bud, root and shoot apex, respectively. More notably, several SlCLEs are dramatically regulated in their transcriptional levels during fruit development and ripening, indicating significant role these genes may potentially play in the critical physiological process. Upon the treatment with synthetic peptides corresponding to the 12-aa CLE domains of SlCLE 10, 12 and 13, tomato seedlings exhibit a clear reduction in root length to varying degrees.

Conclusions: This study provides a comprehensive genomic analysis of CLE gene family in tomato, a crop species with fleshy fruit. Differential expression patterns of various SlCLEs provide important insights into the functional divergence of CLE signaling cascade in Solanaceae species, especially their potential involvements in the regulation of fruit development and ripening.

Show MeSH