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Proteomic analysis of Artemisia annua--towards elucidating the biosynthetic pathways of the antimalarial pro-drug artemisinin.

Bryant L, Flatley B, Patole C, Brown GD, Cramer R - BMC Plant Biol. (2015)

Bottom Line: The comparison of various databases containing A. annua sequences (NCBInr/viridiplantae, UniProt/viridiplantae, UniProt/A. annua, an A. annua trichome Trinity contig database, the above contig database and another A. annua EST database) revealed significant differences in respect of their suitability for proteomic analysis, showing that an organism-specific database that has undergone extensive curation, leading to longer contig sequences, can greatly increase the number of true positive protein identifications, while reducing the number of false positives.The newly gained information allows for the possibility of an enzymatic pathway, utilizing peroxidases, for the less well understood final stages of artemisinin's biosynthesis, as an alternative to the known non-enzymatic in vitro conversion of dihydroartemisinic acid to artemisinin.Data are available via ProteomeXchange with identifier PXD000703.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Whiteknights, Reading, RG6 6AD, United Kingdom. gk002242@reading.ac.uk.

ABSTRACT

Background: MS-based proteomics was applied to the analysis of the medicinal plant Artemisia annua, exploiting a recently published contig sequence database (Graham et al. (2010) Science 327, 328-331) and other genomic and proteomic sequence databases for comparison. A. annua is the predominant natural source of artemisinin, the precursor for artemisinin-based combination therapies (ACTs), which are the WHO-recommended treatment for P. falciparum malaria.

Results: The comparison of various databases containing A. annua sequences (NCBInr/viridiplantae, UniProt/viridiplantae, UniProt/A. annua, an A. annua trichome Trinity contig database, the above contig database and another A. annua EST database) revealed significant differences in respect of their suitability for proteomic analysis, showing that an organism-specific database that has undergone extensive curation, leading to longer contig sequences, can greatly increase the number of true positive protein identifications, while reducing the number of false positives. Compared to previously published data an order-of-magnitude more proteins have been identified from trichome-enriched A. annua samples, including proteins which are known to be involved in the biosynthesis of artemisinin, as well as other highly abundant proteins, which suggest additional enzymatic processes occurring within the trichomes that are important for the biosynthesis of artemisinin.

Conclusions: The newly gained information allows for the possibility of an enzymatic pathway, utilizing peroxidases, for the less well understood final stages of artemisinin's biosynthesis, as an alternative to the known non-enzymatic in vitro conversion of dihydroartemisinic acid to artemisinin. Data are available via ProteomeXchange with identifier PXD000703.

No MeSH data available.


Related in: MedlinePlus

Functional classification (GO terms) of the Masoct-identified proteins from the trichome-enriched sample material, using the UniProtKB database (taxonomoy: viridiplantae). Mascot search results were submitted to Percolator with an ‘expect cut-off’ threshold of 0.05
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Fig1: Functional classification (GO terms) of the Masoct-identified proteins from the trichome-enriched sample material, using the UniProtKB database (taxonomoy: viridiplantae). Mascot search results were submitted to Percolator with an ‘expect cut-off’ threshold of 0.05

Mentions: In general, the vast majority of proteins identified previously from A. annua by Wu et al. were also found in our datasets [10]. Notably, in the trichome-enriched sample data, we found amongst others a similarly large number of ATPases/ATP synthases and oxidoreductases (e.g. four ferredoxins), as well as many proteins involved in translation and transcription and also in proteolysis and the proteosome. Furthermore, several kinases and phosphatases were also identified. Figure 1 displays a rough molecular functional classification (GO terms) of the UniProtKB (taxonomoy: viridiplantae)-identified proteins from the trichome-enriched sample material after submission to Percolator and setting the ‘expect cut-off’ threshold to 0.05.Fig. 1


Proteomic analysis of Artemisia annua--towards elucidating the biosynthetic pathways of the antimalarial pro-drug artemisinin.

Bryant L, Flatley B, Patole C, Brown GD, Cramer R - BMC Plant Biol. (2015)

Functional classification (GO terms) of the Masoct-identified proteins from the trichome-enriched sample material, using the UniProtKB database (taxonomoy: viridiplantae). Mascot search results were submitted to Percolator with an ‘expect cut-off’ threshold of 0.05
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4496932&req=5

Fig1: Functional classification (GO terms) of the Masoct-identified proteins from the trichome-enriched sample material, using the UniProtKB database (taxonomoy: viridiplantae). Mascot search results were submitted to Percolator with an ‘expect cut-off’ threshold of 0.05
Mentions: In general, the vast majority of proteins identified previously from A. annua by Wu et al. were also found in our datasets [10]. Notably, in the trichome-enriched sample data, we found amongst others a similarly large number of ATPases/ATP synthases and oxidoreductases (e.g. four ferredoxins), as well as many proteins involved in translation and transcription and also in proteolysis and the proteosome. Furthermore, several kinases and phosphatases were also identified. Figure 1 displays a rough molecular functional classification (GO terms) of the UniProtKB (taxonomoy: viridiplantae)-identified proteins from the trichome-enriched sample material after submission to Percolator and setting the ‘expect cut-off’ threshold to 0.05.Fig. 1

Bottom Line: The comparison of various databases containing A. annua sequences (NCBInr/viridiplantae, UniProt/viridiplantae, UniProt/A. annua, an A. annua trichome Trinity contig database, the above contig database and another A. annua EST database) revealed significant differences in respect of their suitability for proteomic analysis, showing that an organism-specific database that has undergone extensive curation, leading to longer contig sequences, can greatly increase the number of true positive protein identifications, while reducing the number of false positives.The newly gained information allows for the possibility of an enzymatic pathway, utilizing peroxidases, for the less well understood final stages of artemisinin's biosynthesis, as an alternative to the known non-enzymatic in vitro conversion of dihydroartemisinic acid to artemisinin.Data are available via ProteomeXchange with identifier PXD000703.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Whiteknights, Reading, RG6 6AD, United Kingdom. gk002242@reading.ac.uk.

ABSTRACT

Background: MS-based proteomics was applied to the analysis of the medicinal plant Artemisia annua, exploiting a recently published contig sequence database (Graham et al. (2010) Science 327, 328-331) and other genomic and proteomic sequence databases for comparison. A. annua is the predominant natural source of artemisinin, the precursor for artemisinin-based combination therapies (ACTs), which are the WHO-recommended treatment for P. falciparum malaria.

Results: The comparison of various databases containing A. annua sequences (NCBInr/viridiplantae, UniProt/viridiplantae, UniProt/A. annua, an A. annua trichome Trinity contig database, the above contig database and another A. annua EST database) revealed significant differences in respect of their suitability for proteomic analysis, showing that an organism-specific database that has undergone extensive curation, leading to longer contig sequences, can greatly increase the number of true positive protein identifications, while reducing the number of false positives. Compared to previously published data an order-of-magnitude more proteins have been identified from trichome-enriched A. annua samples, including proteins which are known to be involved in the biosynthesis of artemisinin, as well as other highly abundant proteins, which suggest additional enzymatic processes occurring within the trichomes that are important for the biosynthesis of artemisinin.

Conclusions: The newly gained information allows for the possibility of an enzymatic pathway, utilizing peroxidases, for the less well understood final stages of artemisinin's biosynthesis, as an alternative to the known non-enzymatic in vitro conversion of dihydroartemisinic acid to artemisinin. Data are available via ProteomeXchange with identifier PXD000703.

No MeSH data available.


Related in: MedlinePlus