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Genome-wide identification, molecular cloning, expression profiling and posttranscriptional regulation analysis of the Argonaute gene family in Salvia miltiorrhiza, an emerging model medicinal plant.

Shao F, Lu S - BMC Genomics (2013)

Bottom Line: The results implied that some SmAGOs, such as SmAGO1, SmAGO2, SmAGO3, SmAGO7 and SmAGO10, probably played similar roles as their counterparts in Arabidopsis; whereas the others could be more species-specialized.Using the modified 5'-RACE method, we confirmed that SmAGO1 and SmAGO2 were targeted by S. miltiorrhiza miR168a/b and miR403, respectively.The results provide useful information for further elucidation of gene silencing pathways in S. miltiorrhiza.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No 151, Malianwa North Road, Haidian District, Beijing 100193, China.

ABSTRACT

Background: Argonaute (AGO) is the core component of RNA-induced silencing complex. The AGO gene family has been analyzed in various plant species; however, there is no report about AGOs in the well-known Traditional Chinese Medicine (TCM) plant, Salvia miltiorrhiza.

Results: Through a genome-wide analysis, we identified ten SmAGO genes in S. miltiorrhiza. Full-length cDNAs of all SmAGOs were subsequently cloned and sequenced. These SmAGOs were characterized using a comprehensive approach. Sequence features, gene structures and conserved domains were analyzed by the comparison of SmAGOs and AtAGOs. Phylogenetic relationships among AGO proteins from S. miltiorrhiza, Arabidopsis and rice were revealed. The expression levels of SmAGO genes in various tissues of S. miltiorrhiza were investigated. The results implied that some SmAGOs, such as SmAGO1, SmAGO2, SmAGO3, SmAGO7 and SmAGO10, probably played similar roles as their counterparts in Arabidopsis; whereas the others could be more species-specialized. It suggests the conservation and diversity of AGOs in plants. Additionally, we identified a total of 24 hairpin structures, representing six miRNA gene families, to be miRNA precursors. Using the modified 5'-RACE method, we confirmed that SmAGO1 and SmAGO2 were targeted by S. miltiorrhiza miR168a/b and miR403, respectively. It suggests the conservation of AGO1-miR168 and AGO2-miR403 regulatory modules in S. miltiorrhiza and Arabidopsis.

Conclusions: This is the first attempt to explore SmAGOs and miRNAs in S. miltiorrhiza. The results provide useful information for further elucidation of gene silencing pathways in S. miltiorrhiza.

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Gene structures of AGOs in S. miltiorrhiza. Exons, UTRs, introns and intron phases are shown.
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Figure 1: Gene structures of AGOs in S. miltiorrhiza. Exons, UTRs, introns and intron phases are shown.

Mentions: It is very important to know the correct cDNA sequence for systematic characterization of AGOs in S. miltiorrhiza. In order to confirm the results from prediction and correct errors of computation, molecular cloning of full-length SmAGO cDNA was carried out. As a result, all of ten predicted SmAGO genes were experimentally validated. Analysis of sequence features showed that the length of open reading frames (ORFs) of SmAGOs varied from 2,472 (SmAGO5) to 3,195 bp (SmAGO1) (Table 1). The length of 5′ and 3′ UTRs was between 30 and 202 bp and between 91 and 337 bp, respectively. The size of deduced SmAGO proteins varied between 823 and 1064 amino acids, the molecular weight (Mw) varied from 93.2 to 118.7 kDa, and the theoretical pI was between 9 and 10 (Table 1). These sequence features are quite similar to that of AtAGOs in Arabidopsis (Table 2). The similarity between SmAGOs and AtAGOs was also observed in gene structures. Many SmAGOs genes have the number and phase of introns similar to an AtAGO, such as SmAGO1/AtAGO1, SmAGO4/AtAGO4, SmAGO7/AtAGO7, SmAGO8/AtAGO8, and SmAGO9/AtAGO9 (Tables 1 and 2, Figures 1 and 2). Additionally, both SmAGO6/AtAGO6 and SmAGO9/AtAGO9 have an intron in 3′ UTR (Figures 1 and 2). The results suggest the conservation between SmAGOs and AtAGOs.


Genome-wide identification, molecular cloning, expression profiling and posttranscriptional regulation analysis of the Argonaute gene family in Salvia miltiorrhiza, an emerging model medicinal plant.

Shao F, Lu S - BMC Genomics (2013)

Gene structures of AGOs in S. miltiorrhiza. Exons, UTRs, introns and intron phases are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750313&req=5

Figure 1: Gene structures of AGOs in S. miltiorrhiza. Exons, UTRs, introns and intron phases are shown.
Mentions: It is very important to know the correct cDNA sequence for systematic characterization of AGOs in S. miltiorrhiza. In order to confirm the results from prediction and correct errors of computation, molecular cloning of full-length SmAGO cDNA was carried out. As a result, all of ten predicted SmAGO genes were experimentally validated. Analysis of sequence features showed that the length of open reading frames (ORFs) of SmAGOs varied from 2,472 (SmAGO5) to 3,195 bp (SmAGO1) (Table 1). The length of 5′ and 3′ UTRs was between 30 and 202 bp and between 91 and 337 bp, respectively. The size of deduced SmAGO proteins varied between 823 and 1064 amino acids, the molecular weight (Mw) varied from 93.2 to 118.7 kDa, and the theoretical pI was between 9 and 10 (Table 1). These sequence features are quite similar to that of AtAGOs in Arabidopsis (Table 2). The similarity between SmAGOs and AtAGOs was also observed in gene structures. Many SmAGOs genes have the number and phase of introns similar to an AtAGO, such as SmAGO1/AtAGO1, SmAGO4/AtAGO4, SmAGO7/AtAGO7, SmAGO8/AtAGO8, and SmAGO9/AtAGO9 (Tables 1 and 2, Figures 1 and 2). Additionally, both SmAGO6/AtAGO6 and SmAGO9/AtAGO9 have an intron in 3′ UTR (Figures 1 and 2). The results suggest the conservation between SmAGOs and AtAGOs.

Bottom Line: The results implied that some SmAGOs, such as SmAGO1, SmAGO2, SmAGO3, SmAGO7 and SmAGO10, probably played similar roles as their counterparts in Arabidopsis; whereas the others could be more species-specialized.Using the modified 5'-RACE method, we confirmed that SmAGO1 and SmAGO2 were targeted by S. miltiorrhiza miR168a/b and miR403, respectively.The results provide useful information for further elucidation of gene silencing pathways in S. miltiorrhiza.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No 151, Malianwa North Road, Haidian District, Beijing 100193, China.

ABSTRACT

Background: Argonaute (AGO) is the core component of RNA-induced silencing complex. The AGO gene family has been analyzed in various plant species; however, there is no report about AGOs in the well-known Traditional Chinese Medicine (TCM) plant, Salvia miltiorrhiza.

Results: Through a genome-wide analysis, we identified ten SmAGO genes in S. miltiorrhiza. Full-length cDNAs of all SmAGOs were subsequently cloned and sequenced. These SmAGOs were characterized using a comprehensive approach. Sequence features, gene structures and conserved domains were analyzed by the comparison of SmAGOs and AtAGOs. Phylogenetic relationships among AGO proteins from S. miltiorrhiza, Arabidopsis and rice were revealed. The expression levels of SmAGO genes in various tissues of S. miltiorrhiza were investigated. The results implied that some SmAGOs, such as SmAGO1, SmAGO2, SmAGO3, SmAGO7 and SmAGO10, probably played similar roles as their counterparts in Arabidopsis; whereas the others could be more species-specialized. It suggests the conservation and diversity of AGOs in plants. Additionally, we identified a total of 24 hairpin structures, representing six miRNA gene families, to be miRNA precursors. Using the modified 5'-RACE method, we confirmed that SmAGO1 and SmAGO2 were targeted by S. miltiorrhiza miR168a/b and miR403, respectively. It suggests the conservation of AGO1-miR168 and AGO2-miR403 regulatory modules in S. miltiorrhiza and Arabidopsis.

Conclusions: This is the first attempt to explore SmAGOs and miRNAs in S. miltiorrhiza. The results provide useful information for further elucidation of gene silencing pathways in S. miltiorrhiza.

Show MeSH