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Comparative metaproteomic analysis on consecutively Rehmannia glutinosa-monocultured rhizosphere soil.

Wu L, Wang H, Zhang Z, Lin R, Zhang Z, Lin W - PLoS ONE (2011)

Bottom Line: The consecutive monoculture for most of medicinal plants, such as Rehmannia glutinosa, results in a significant reduction in the yield and quality.The results suggest that the consecutive monoculture of R. glutinosa changes the soil microbial ecology due to the exudates accumulation, as a result, the nutrient cycles are affected, leading to the retardation of plant growth and development.Our results demonstrated the interactions among plant, soil and microflora in the proteomic level are crucial for the productivity and quality of R. glutinosa in consecutive monoculture system.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.

ABSTRACT

Background: The consecutive monoculture for most of medicinal plants, such as Rehmannia glutinosa, results in a significant reduction in the yield and quality. There is an urgent need to study for the sustainable development of Chinese herbaceous medicine.

Methodology/principal findings: Comparative metaproteomics of rhizosphere soil was developed and used to analyze the underlying mechanism of the consecutive monoculture problems of R. glutinosa. The 2D-gel patterns of protein spots for the soil samples showed a strong matrix dependency. Among the spots, 103 spots with high resolution and repeatability were randomly selected and successfully identified by MALDI TOF-TOF MS for a rhizosphere soil metaproteomic profile analysis. These proteins originating from plants and microorganisms play important roles in nutrient cycles and energy flow in rhizospheric soil ecosystem. They function in protein, nucleotide and secondary metabolisms, signal transduction and resistance. Comparative metaproteomics analysis revealed 33 differentially expressed protein spots in rhizosphere soil in response to increasing years of monoculture. Among them, plant proteins related to carbon and nitrogen metabolism and stress response, were mostly up-regulated except a down-regulated protein (glutathione S-transferase) involving detoxification. The phenylalanine ammonia-lyase was believed to participate in the phenylpropanoid metabolism as shown with a considerable increase in total phenolic acid content with increasing years of monoculture. Microbial proteins related to protein metabolism and cell wall biosynthesis, were up-regulated except a down-regulated protein (geranylgeranyl pyrophosphate synthase) functioning in diterpenoid synthesis. The results suggest that the consecutive monoculture of R. glutinosa changes the soil microbial ecology due to the exudates accumulation, as a result, the nutrient cycles are affected, leading to the retardation of plant growth and development.

Conclusions/significance: Our results demonstrated the interactions among plant, soil and microflora in the proteomic level are crucial for the productivity and quality of R. glutinosa in consecutive monoculture system.

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Related in: MedlinePlus

Representative MS spectra of proteins identified by MALDI TOF-TOF MS.Protein Spot 10 was excised from gels, and spectrum of peptides derived after tryptic digestion. (A) MS spectrum of Ion 1453.775 was analyzed by MS/MS. (B) TOF/TOF spectrum of Ion 1453.775. (C) Tandem mass spectrum that confirmed the responding amino acid sequence, FVIGGPHGDAGLTGR, by analyzing b- and y-ions derived from the peptide ion.
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pone-0020611-g003: Representative MS spectra of proteins identified by MALDI TOF-TOF MS.Protein Spot 10 was excised from gels, and spectrum of peptides derived after tryptic digestion. (A) MS spectrum of Ion 1453.775 was analyzed by MS/MS. (B) TOF/TOF spectrum of Ion 1453.775. (C) Tandem mass spectrum that confirmed the responding amino acid sequence, FVIGGPHGDAGLTGR, by analyzing b- and y-ions derived from the peptide ion.

Mentions: To obtain a metaproteomic profile for the R. glutinosa rhizosphere soil, 152 protein spots with high resolution and repeatability were randomly selected and excised from the prepared gels, digested in-gel with trypsin, and 103 protein spots were successfully analyzed by LIFT-MALDI TOF-TOF MS (Figure 2, 3). This meant that 49 protein spots failed to be identified by MS maybe due to the excision process not producing usable data or the incomplete environmental metaproteome databases. Database searching was conducted with the BioTools 3.1 software and MASCOT 2.2.03 search engine, firstly against all entries on NCBInr and followed by the ‘Bacteria’ and ‘Fungi’ database. Thirty-four proteins sharing equal searching by MS/MS and MS against all entries are listed in Table S1. Forty-one proteins matched at least 2 MS/MS peptides are listed in Table S2. Twenty-eight proteins matched at least 3 peptide mass fingerprintings (PMFs) are listed in Table S3.


Comparative metaproteomic analysis on consecutively Rehmannia glutinosa-monocultured rhizosphere soil.

Wu L, Wang H, Zhang Z, Lin R, Zhang Z, Lin W - PLoS ONE (2011)

Representative MS spectra of proteins identified by MALDI TOF-TOF MS.Protein Spot 10 was excised from gels, and spectrum of peptides derived after tryptic digestion. (A) MS spectrum of Ion 1453.775 was analyzed by MS/MS. (B) TOF/TOF spectrum of Ion 1453.775. (C) Tandem mass spectrum that confirmed the responding amino acid sequence, FVIGGPHGDAGLTGR, by analyzing b- and y-ions derived from the peptide ion.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3105091&req=5

pone-0020611-g003: Representative MS spectra of proteins identified by MALDI TOF-TOF MS.Protein Spot 10 was excised from gels, and spectrum of peptides derived after tryptic digestion. (A) MS spectrum of Ion 1453.775 was analyzed by MS/MS. (B) TOF/TOF spectrum of Ion 1453.775. (C) Tandem mass spectrum that confirmed the responding amino acid sequence, FVIGGPHGDAGLTGR, by analyzing b- and y-ions derived from the peptide ion.
Mentions: To obtain a metaproteomic profile for the R. glutinosa rhizosphere soil, 152 protein spots with high resolution and repeatability were randomly selected and excised from the prepared gels, digested in-gel with trypsin, and 103 protein spots were successfully analyzed by LIFT-MALDI TOF-TOF MS (Figure 2, 3). This meant that 49 protein spots failed to be identified by MS maybe due to the excision process not producing usable data or the incomplete environmental metaproteome databases. Database searching was conducted with the BioTools 3.1 software and MASCOT 2.2.03 search engine, firstly against all entries on NCBInr and followed by the ‘Bacteria’ and ‘Fungi’ database. Thirty-four proteins sharing equal searching by MS/MS and MS against all entries are listed in Table S1. Forty-one proteins matched at least 2 MS/MS peptides are listed in Table S2. Twenty-eight proteins matched at least 3 peptide mass fingerprintings (PMFs) are listed in Table S3.

Bottom Line: The consecutive monoculture for most of medicinal plants, such as Rehmannia glutinosa, results in a significant reduction in the yield and quality.The results suggest that the consecutive monoculture of R. glutinosa changes the soil microbial ecology due to the exudates accumulation, as a result, the nutrient cycles are affected, leading to the retardation of plant growth and development.Our results demonstrated the interactions among plant, soil and microflora in the proteomic level are crucial for the productivity and quality of R. glutinosa in consecutive monoculture system.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.

ABSTRACT

Background: The consecutive monoculture for most of medicinal plants, such as Rehmannia glutinosa, results in a significant reduction in the yield and quality. There is an urgent need to study for the sustainable development of Chinese herbaceous medicine.

Methodology/principal findings: Comparative metaproteomics of rhizosphere soil was developed and used to analyze the underlying mechanism of the consecutive monoculture problems of R. glutinosa. The 2D-gel patterns of protein spots for the soil samples showed a strong matrix dependency. Among the spots, 103 spots with high resolution and repeatability were randomly selected and successfully identified by MALDI TOF-TOF MS for a rhizosphere soil metaproteomic profile analysis. These proteins originating from plants and microorganisms play important roles in nutrient cycles and energy flow in rhizospheric soil ecosystem. They function in protein, nucleotide and secondary metabolisms, signal transduction and resistance. Comparative metaproteomics analysis revealed 33 differentially expressed protein spots in rhizosphere soil in response to increasing years of monoculture. Among them, plant proteins related to carbon and nitrogen metabolism and stress response, were mostly up-regulated except a down-regulated protein (glutathione S-transferase) involving detoxification. The phenylalanine ammonia-lyase was believed to participate in the phenylpropanoid metabolism as shown with a considerable increase in total phenolic acid content with increasing years of monoculture. Microbial proteins related to protein metabolism and cell wall biosynthesis, were up-regulated except a down-regulated protein (geranylgeranyl pyrophosphate synthase) functioning in diterpenoid synthesis. The results suggest that the consecutive monoculture of R. glutinosa changes the soil microbial ecology due to the exudates accumulation, as a result, the nutrient cycles are affected, leading to the retardation of plant growth and development.

Conclusions/significance: Our results demonstrated the interactions among plant, soil and microflora in the proteomic level are crucial for the productivity and quality of R. glutinosa in consecutive monoculture system.

Show MeSH
Related in: MedlinePlus