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Computational Identification and Systematic Classification of Novel Cytochrome P450 Genes in Salvia miltiorrhiza.

Chen H, Wu B, Nelson DR, Wu K, Liu C - PLoS ONE (2014)

Bottom Line: The RNA-Seq results showed that 35 CYP450 genes were co-expressed with CYP76AH1, a marker gene for tanshinone biosynthesis, using r≥0.9 as a cutoff.Comparing against the KEGG database, 10 CYP450 genes were found to be associated with diterpenoid biosynthesis.Moreover, we found that 15 CYP450 genes were possibly regulated by antisense transcripts (r≥0.9 or r≤-0.9).

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

ABSTRACT
Salvia miltiorrhiza is one of the most economically important medicinal plants. Cytochrome P450 (CYP450) genes have been implicated in the biosynthesis of its active components. However, only a dozen full-length CYP450 genes have been described, and there is no systematic classification of CYP450 genes in S. miltiorrhiza. We obtained 77,549 unigenes from three tissue types of S. miltiorrhiza using RNA-Seq technology. Combining our data with previously identified CYP450 sequences and scanning with the CYP450 model from Pfam resulted in the identification of 116 full-length and 135 partial-length CYP450 genes. The 116 genes were classified into 9 clans and 38 families using standard criteria. The RNA-Seq results showed that 35 CYP450 genes were co-expressed with CYP76AH1, a marker gene for tanshinone biosynthesis, using r≥0.9 as a cutoff. The expression profiles for 16 of 19 randomly selected CYP450 obtained from RNA-Seq were validated by qRT-PCR. Comparing against the KEGG database, 10 CYP450 genes were found to be associated with diterpenoid biosynthesis. Considering all the evidence, 3 CYP450 genes were identified to be potentially involved in terpenoid biosynthesis. Moreover, we found that 15 CYP450 genes were possibly regulated by antisense transcripts (r≥0.9 or r≤-0.9). Lastly, a web resource (SMCYP450, http://www.herbalgenomics.org/samicyp450) was set up, which allows users to browse, search, retrieve and compare CYP450 genes and can serve as a centralized resource.

No MeSH data available.


KEGG pathway analyses of predicted CYP450 genes in S. miltiorrhiza.The numbers of CYP450 genes involved in the corresponding metabolic processes are shown.
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pone-0115149-g006: KEGG pathway analyses of predicted CYP450 genes in S. miltiorrhiza.The numbers of CYP450 genes involved in the corresponding metabolic processes are shown.

Mentions: Pathway-based analysis was performed, as described in the methods section, to further understand the biological functions and interactions of the CYP450 genes. In total, 49 (44.2%) CYP450 proteins were assigned to 14 KEGG pathways, of which two were the monoterpenoid and diterpenoid biosynthesis pathways (Fig. 6). Particularly, 14 CYP450s were found to be involved in the monoterpenoid biosynthesis, including SmCYP71D410, SmCYP71D411, SmCYP71D374, SmCYP71D412, SmCYP71D413, SmCYP71AU52, SmCYP71A59, SmCYP71A57, SmCYP71A58, SmCYP71AU53, SmCYP81B62, SmCYP98A75, SmCYP98A76 and SmCYP98A77. Among them, 10 belonged to the CYP71 family, 3 belonged to the CYP98 family and 1 belonged to the CYP81 family. In contrast, 10 CYP450s were mapped to the diterpenoid biosynthesis pathway, including SmCYP716A89, SmCYP716D25, SmCYP728D17, SmCYP76A35, SmCYP76S7, SmCYP76AK2, SmCYP76AK3, SmCYP76AH1, SmCYP76G16 and SmCYP701A40. Among them, 2 belonged to the CYP716 family, 1 belonged to the CYP728 family, 6 belonged to the CYP76 family and 1 belonged to the CYP701 family. CYP701 is involved in the biosynthesis of gibberellins, which are diterpenoid acids [37]. These CYP450s are likely to be involved in these terpenoid biosynthesis pathways, and future experiments are required to test this hypothesis.


Computational Identification and Systematic Classification of Novel Cytochrome P450 Genes in Salvia miltiorrhiza.

Chen H, Wu B, Nelson DR, Wu K, Liu C - PLoS ONE (2014)

KEGG pathway analyses of predicted CYP450 genes in S. miltiorrhiza.The numbers of CYP450 genes involved in the corresponding metabolic processes are shown.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4262458&req=5

pone-0115149-g006: KEGG pathway analyses of predicted CYP450 genes in S. miltiorrhiza.The numbers of CYP450 genes involved in the corresponding metabolic processes are shown.
Mentions: Pathway-based analysis was performed, as described in the methods section, to further understand the biological functions and interactions of the CYP450 genes. In total, 49 (44.2%) CYP450 proteins were assigned to 14 KEGG pathways, of which two were the monoterpenoid and diterpenoid biosynthesis pathways (Fig. 6). Particularly, 14 CYP450s were found to be involved in the monoterpenoid biosynthesis, including SmCYP71D410, SmCYP71D411, SmCYP71D374, SmCYP71D412, SmCYP71D413, SmCYP71AU52, SmCYP71A59, SmCYP71A57, SmCYP71A58, SmCYP71AU53, SmCYP81B62, SmCYP98A75, SmCYP98A76 and SmCYP98A77. Among them, 10 belonged to the CYP71 family, 3 belonged to the CYP98 family and 1 belonged to the CYP81 family. In contrast, 10 CYP450s were mapped to the diterpenoid biosynthesis pathway, including SmCYP716A89, SmCYP716D25, SmCYP728D17, SmCYP76A35, SmCYP76S7, SmCYP76AK2, SmCYP76AK3, SmCYP76AH1, SmCYP76G16 and SmCYP701A40. Among them, 2 belonged to the CYP716 family, 1 belonged to the CYP728 family, 6 belonged to the CYP76 family and 1 belonged to the CYP701 family. CYP701 is involved in the biosynthesis of gibberellins, which are diterpenoid acids [37]. These CYP450s are likely to be involved in these terpenoid biosynthesis pathways, and future experiments are required to test this hypothesis.

Bottom Line: The RNA-Seq results showed that 35 CYP450 genes were co-expressed with CYP76AH1, a marker gene for tanshinone biosynthesis, using r≥0.9 as a cutoff.Comparing against the KEGG database, 10 CYP450 genes were found to be associated with diterpenoid biosynthesis.Moreover, we found that 15 CYP450 genes were possibly regulated by antisense transcripts (r≥0.9 or r≤-0.9).

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

ABSTRACT
Salvia miltiorrhiza is one of the most economically important medicinal plants. Cytochrome P450 (CYP450) genes have been implicated in the biosynthesis of its active components. However, only a dozen full-length CYP450 genes have been described, and there is no systematic classification of CYP450 genes in S. miltiorrhiza. We obtained 77,549 unigenes from three tissue types of S. miltiorrhiza using RNA-Seq technology. Combining our data with previously identified CYP450 sequences and scanning with the CYP450 model from Pfam resulted in the identification of 116 full-length and 135 partial-length CYP450 genes. The 116 genes were classified into 9 clans and 38 families using standard criteria. The RNA-Seq results showed that 35 CYP450 genes were co-expressed with CYP76AH1, a marker gene for tanshinone biosynthesis, using r≥0.9 as a cutoff. The expression profiles for 16 of 19 randomly selected CYP450 obtained from RNA-Seq were validated by qRT-PCR. Comparing against the KEGG database, 10 CYP450 genes were found to be associated with diterpenoid biosynthesis. Considering all the evidence, 3 CYP450 genes were identified to be potentially involved in terpenoid biosynthesis. Moreover, we found that 15 CYP450 genes were possibly regulated by antisense transcripts (r≥0.9 or r≤-0.9). Lastly, a web resource (SMCYP450, http://www.herbalgenomics.org/samicyp450) was set up, which allows users to browse, search, retrieve and compare CYP450 genes and can serve as a centralized resource.

No MeSH data available.