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Exoproteome analysis of Clostridium cellulovorans in natural soft-biomass degradation.

Esaka K, Aburaya S, Morisaka H, Kuroda K, Ueda M - AMB Express (2015)

Bottom Line: Its excellent capacity for degradation results from optimization of the composition of the protein complex (cellulosome) and production of non-cellulosomal proteins according to the type of substrates.Using an isobaric tag method and a liquid chromatograph equipped with a long monolithic silica capillary column/mass spectrometer, we identified 372 proteins in the culture supernatant.Of these, we focused on 77 saccharification-related proteins of both cellulosomal and non-cellulosomal origins.

View Article: PubMed Central - PubMed

Affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto Japan.

ABSTRACT

Clostridium cellulovorans is an anaerobic, cellulolytic bacterium, capable of effectively degrading various types of soft biomass. Its excellent capacity for degradation results from optimization of the composition of the protein complex (cellulosome) and production of non-cellulosomal proteins according to the type of substrates. In this study, we performed a quantitative proteome analysis to determine changes in the extracellular proteins produced by C. cellulovorans for degradation of several types of natural soft biomass. C. cellulovorans was cultured in media containing bagasse, corn germ, rice straw (natural soft biomass), or cellobiose (control). Using an isobaric tag method and a liquid chromatograph equipped with a long monolithic silica capillary column/mass spectrometer, we identified 372 proteins in the culture supernatant. Of these, we focused on 77 saccharification-related proteins of both cellulosomal and non-cellulosomal origins. Statistical analysis showed that 18 of the proteins were specifically produced during degradation of types of natural soft biomass. Interestingly, the protein Clocel_3197 was found and commonly involved in the degradation of every natural soft biomass studied. This protein may perform functions, in addition to its known metabolic functions, that contribute to effective degradation of natural soft biomass.

No MeSH data available.


Related in: MedlinePlus

Statistical analysis for detection of proteins specific for degradation of each natural soft biomass type. The total number of proteins identified and the number of proteins involved in saccharification are shown. A total of 372 proteins were initially quantified. To confirm reproducibility, scatter plots of the quantitative values were created, and principal component analysis was performed (Additional files 2, 3). For detection of specific proteins for natural soft biomass degradation, 77 cellulosomal and non-cellulosomal proteins were selected from the 372 proteins identified. To determine which proteins were biomass-specific, empirical Bayes moderated t-tests were performed and volcano plots were generated (Figure 3A).
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Fig2: Statistical analysis for detection of proteins specific for degradation of each natural soft biomass type. The total number of proteins identified and the number of proteins involved in saccharification are shown. A total of 372 proteins were initially quantified. To confirm reproducibility, scatter plots of the quantitative values were created, and principal component analysis was performed (Additional files 2, 3). For detection of specific proteins for natural soft biomass degradation, 77 cellulosomal and non-cellulosomal proteins were selected from the 372 proteins identified. To determine which proteins were biomass-specific, empirical Bayes moderated t-tests were performed and volcano plots were generated (Figure 3A).

Mentions: To investigate the degradation of natural soft biomass, proteins were isolated from the supernatant of stationary-phase C. cellulovorans cultures grown on bagasse, corn germ, or rice straw, and subjected to LC-MS/MS analysis (Figure 1) (Matsui et al. 2013). The mass spectrometry data collected were used for exoproteome analysis, as shown in Figure 2.Figure 1


Exoproteome analysis of Clostridium cellulovorans in natural soft-biomass degradation.

Esaka K, Aburaya S, Morisaka H, Kuroda K, Ueda M - AMB Express (2015)

Statistical analysis for detection of proteins specific for degradation of each natural soft biomass type. The total number of proteins identified and the number of proteins involved in saccharification are shown. A total of 372 proteins were initially quantified. To confirm reproducibility, scatter plots of the quantitative values were created, and principal component analysis was performed (Additional files 2, 3). For detection of specific proteins for natural soft biomass degradation, 77 cellulosomal and non-cellulosomal proteins were selected from the 372 proteins identified. To determine which proteins were biomass-specific, empirical Bayes moderated t-tests were performed and volcano plots were generated (Figure 3A).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4305082&req=5

Fig2: Statistical analysis for detection of proteins specific for degradation of each natural soft biomass type. The total number of proteins identified and the number of proteins involved in saccharification are shown. A total of 372 proteins were initially quantified. To confirm reproducibility, scatter plots of the quantitative values were created, and principal component analysis was performed (Additional files 2, 3). For detection of specific proteins for natural soft biomass degradation, 77 cellulosomal and non-cellulosomal proteins were selected from the 372 proteins identified. To determine which proteins were biomass-specific, empirical Bayes moderated t-tests were performed and volcano plots were generated (Figure 3A).
Mentions: To investigate the degradation of natural soft biomass, proteins were isolated from the supernatant of stationary-phase C. cellulovorans cultures grown on bagasse, corn germ, or rice straw, and subjected to LC-MS/MS analysis (Figure 1) (Matsui et al. 2013). The mass spectrometry data collected were used for exoproteome analysis, as shown in Figure 2.Figure 1

Bottom Line: Its excellent capacity for degradation results from optimization of the composition of the protein complex (cellulosome) and production of non-cellulosomal proteins according to the type of substrates.Using an isobaric tag method and a liquid chromatograph equipped with a long monolithic silica capillary column/mass spectrometer, we identified 372 proteins in the culture supernatant.Of these, we focused on 77 saccharification-related proteins of both cellulosomal and non-cellulosomal origins.

View Article: PubMed Central - PubMed

Affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto Japan.

ABSTRACT

Clostridium cellulovorans is an anaerobic, cellulolytic bacterium, capable of effectively degrading various types of soft biomass. Its excellent capacity for degradation results from optimization of the composition of the protein complex (cellulosome) and production of non-cellulosomal proteins according to the type of substrates. In this study, we performed a quantitative proteome analysis to determine changes in the extracellular proteins produced by C. cellulovorans for degradation of several types of natural soft biomass. C. cellulovorans was cultured in media containing bagasse, corn germ, rice straw (natural soft biomass), or cellobiose (control). Using an isobaric tag method and a liquid chromatograph equipped with a long monolithic silica capillary column/mass spectrometer, we identified 372 proteins in the culture supernatant. Of these, we focused on 77 saccharification-related proteins of both cellulosomal and non-cellulosomal origins. Statistical analysis showed that 18 of the proteins were specifically produced during degradation of types of natural soft biomass. Interestingly, the protein Clocel_3197 was found and commonly involved in the degradation of every natural soft biomass studied. This protein may perform functions, in addition to its known metabolic functions, that contribute to effective degradation of natural soft biomass.

No MeSH data available.


Related in: MedlinePlus