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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.


Related in: MedlinePlus

Weblogos of conserved motifs identified in the 116 CYP450s from S. miltiorrhiza.The names of the motifs are shown above each logo.
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pone-0115149-g005: Weblogos of conserved motifs identified in the 116 CYP450s from S. miltiorrhiza.The names of the motifs are shown above each logo.

Mentions: All CYP450 protein sequences have four distinct characteristics, including the cytochrome P450 cysteine heme-iron ligand signature motif, the PERF motif, the conserved EXXR motif located in the K-helix, and the I-helix, which contains a highly conserved threonine involved in oxygen activation [26], [35]. S. miltiorrhiza CYP450 proteins were subjected to MEME analysis to identify these motifs. The identified motifs were aligned using MAST and presented using WEBLOGO (Fig. 5). The consensus sequences of the heme-binding regions of A-type and non-A-type CYP450s are “PFGXGRRXCXG” and “XFXXGXRXCXG”, respectively. Similarly, the PERF motifs of A-type and non-A-type CYP450s are also different in their consensus sequences, “PERF” and “PXRX”, respectively [36]. In S. miltiorrhiza, the conserved motifs are likely to be “FXPERF” and “FXPXRX” for A-type and non-A-type sequences, respectively, having one additional highly conserved amino acid “F” at the −2 position of the previously described PERF motifs. However, the functional importance of this amino acid remains to be determined. The K-helix motifs of A-type and non-A-type CYP450s are similar to each other, with the sequence “EXXR”. In contrast, the I-helix motifs of A-type and non-A-type CYP450s are likely to be “AGXDT” and “AGX (E/D) T”. The consensus sequences of these motifs are similar to those that have previously been described.


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)

Weblogos of conserved motifs identified in the 116 CYP450s from S. miltiorrhiza.The names of the motifs are shown above each logo.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0115149-g005: Weblogos of conserved motifs identified in the 116 CYP450s from S. miltiorrhiza.The names of the motifs are shown above each logo.
Mentions: All CYP450 protein sequences have four distinct characteristics, including the cytochrome P450 cysteine heme-iron ligand signature motif, the PERF motif, the conserved EXXR motif located in the K-helix, and the I-helix, which contains a highly conserved threonine involved in oxygen activation [26], [35]. S. miltiorrhiza CYP450 proteins were subjected to MEME analysis to identify these motifs. The identified motifs were aligned using MAST and presented using WEBLOGO (Fig. 5). The consensus sequences of the heme-binding regions of A-type and non-A-type CYP450s are “PFGXGRRXCXG” and “XFXXGXRXCXG”, respectively. Similarly, the PERF motifs of A-type and non-A-type CYP450s are also different in their consensus sequences, “PERF” and “PXRX”, respectively [36]. In S. miltiorrhiza, the conserved motifs are likely to be “FXPERF” and “FXPXRX” for A-type and non-A-type sequences, respectively, having one additional highly conserved amino acid “F” at the −2 position of the previously described PERF motifs. However, the functional importance of this amino acid remains to be determined. The K-helix motifs of A-type and non-A-type CYP450s are similar to each other, with the sequence “EXXR”. In contrast, the I-helix motifs of A-type and non-A-type CYP450s are likely to be “AGXDT” and “AGX (E/D) T”. The consensus sequences of these motifs are similar to those that have previously been described.

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.


Related in: MedlinePlus