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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.

Show MeSH
Unrooted neighbor-joining phylogenetic tree of AGOs from S. miltiorrhiza, Arabidopsis and rice. The deduced full-length amino acid sequences were aligned using ClustalW version 1.83 and the phylogenetic tree was constructed using MEGA 4.0 by the neighbor-joining (NJ) method with 1000 bootstrap replicates. Four subgroups, including AGO1, MEL1, AGO4 and ZIPPY, are indicated. SmAGOs are shown in bold.
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Figure 3: Unrooted neighbor-joining phylogenetic tree of AGOs from S. miltiorrhiza, Arabidopsis and rice. The deduced full-length amino acid sequences were aligned using ClustalW version 1.83 and the phylogenetic tree was constructed using MEGA 4.0 by the neighbor-joining (NJ) method with 1000 bootstrap replicates. Four subgroups, including AGO1, MEL1, AGO4 and ZIPPY, are indicated. SmAGOs are shown in bold.

Mentions: Phylogenetic analysis using the PAZ and PIWI domains for rice, Arabidopsis, Caenorhabditis elegans, Drosophila melanogaster, and mouse had previously revealed that animal AGOs clustered into two subgroups: A1 and A2, whereas all plant AGOs could be divided into four subgroups: AGO1, ZIPPY, AGO4, and MEL1 [33]. The AGO1 and MEL1 subgroups had a common lineage with A1, whereas plant ZIPPY and AGO4 subgroups and animal A2 subgroup could be diverged from an ancestral lineage [11]. In order to determine the evolutionary relationship of S. miltiorrhiza AGOs, full-length AGO protein sequences from S. miltiorrhiza, Arabidopsis and rice were aligned and an unrooted neighbor-joining tree was constructed. The results showed that ten SmAGOs could also be divided into four subgroups (FigureĀ 3). Moreover, the clustering remained similar when only the PAZ and PIWI protein domains were used for phylogenetic analysis (data not shown). SmAGO1 and SmAGO10 are included in the AGO1 subgroup with Arabidopsis AtAGO1 and AtAGO10, and rice OsAGO1a-OsAGO1d and OsPNH1. SmAGO1 shares high similarity with AtAGO1 associated with the action of miRNAs, ta-siRNAs and transgene-derived siRNAs [14], whereas SmAGO10 is highly similar to AtAGO10 modulating shoot apical meristem maintenance and establishment of leaf polarity [20]. SmAGO2, SmAGO3 and SmAGO7 are members of the subgroup ZIPPY. Similarly, three Arabidopsis AGOs, including antiviral defense-associated AtAGO2, function-unknown AtAGO3 and AtAGO7 involved in the generation of ta-siRNAs from TAS3[15], are also included in this subgroup. SmAGO7 shares greater similarity with AtAGO7. SmAGO2 and SmAGO3 are highly similar to AtAGO2 and AtAGO3. The MEL1 subgroup contains only one S. miltiorrhiza AGO, SmAGO5, which is similar to the function-unknown Arabidopsis AtAGO5. On the contrary, the AGO4 subgroup is the biggest among four plant AGO subgroups. It contains five S. miltiorrhiza AGOs, including SmAGO4, SmAGO6, SmAGO8 and SmAGO9.


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)

Unrooted neighbor-joining phylogenetic tree of AGOs from S. miltiorrhiza, Arabidopsis and rice. The deduced full-length amino acid sequences were aligned using ClustalW version 1.83 and the phylogenetic tree was constructed using MEGA 4.0 by the neighbor-joining (NJ) method with 1000 bootstrap replicates. Four subgroups, including AGO1, MEL1, AGO4 and ZIPPY, are indicated. SmAGOs are shown in bold.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Unrooted neighbor-joining phylogenetic tree of AGOs from S. miltiorrhiza, Arabidopsis and rice. The deduced full-length amino acid sequences were aligned using ClustalW version 1.83 and the phylogenetic tree was constructed using MEGA 4.0 by the neighbor-joining (NJ) method with 1000 bootstrap replicates. Four subgroups, including AGO1, MEL1, AGO4 and ZIPPY, are indicated. SmAGOs are shown in bold.
Mentions: Phylogenetic analysis using the PAZ and PIWI domains for rice, Arabidopsis, Caenorhabditis elegans, Drosophila melanogaster, and mouse had previously revealed that animal AGOs clustered into two subgroups: A1 and A2, whereas all plant AGOs could be divided into four subgroups: AGO1, ZIPPY, AGO4, and MEL1 [33]. The AGO1 and MEL1 subgroups had a common lineage with A1, whereas plant ZIPPY and AGO4 subgroups and animal A2 subgroup could be diverged from an ancestral lineage [11]. In order to determine the evolutionary relationship of S. miltiorrhiza AGOs, full-length AGO protein sequences from S. miltiorrhiza, Arabidopsis and rice were aligned and an unrooted neighbor-joining tree was constructed. The results showed that ten SmAGOs could also be divided into four subgroups (FigureĀ 3). Moreover, the clustering remained similar when only the PAZ and PIWI protein domains were used for phylogenetic analysis (data not shown). SmAGO1 and SmAGO10 are included in the AGO1 subgroup with Arabidopsis AtAGO1 and AtAGO10, and rice OsAGO1a-OsAGO1d and OsPNH1. SmAGO1 shares high similarity with AtAGO1 associated with the action of miRNAs, ta-siRNAs and transgene-derived siRNAs [14], whereas SmAGO10 is highly similar to AtAGO10 modulating shoot apical meristem maintenance and establishment of leaf polarity [20]. SmAGO2, SmAGO3 and SmAGO7 are members of the subgroup ZIPPY. Similarly, three Arabidopsis AGOs, including antiviral defense-associated AtAGO2, function-unknown AtAGO3 and AtAGO7 involved in the generation of ta-siRNAs from TAS3[15], are also included in this subgroup. SmAGO7 shares greater similarity with AtAGO7. SmAGO2 and SmAGO3 are highly similar to AtAGO2 and AtAGO3. The MEL1 subgroup contains only one S. miltiorrhiza AGO, SmAGO5, which is similar to the function-unknown Arabidopsis AtAGO5. On the contrary, the AGO4 subgroup is the biggest among four plant AGO subgroups. It contains five S. miltiorrhiza AGOs, including SmAGO4, SmAGO6, SmAGO8 and SmAGO9.

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