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Comparison of the mesophilic cellulosome-producing Clostridium cellulovorans genome with other cellulosome-related clostridial genomes.

Tamaru Y, Miyake H, Kuroda K, Nakanishi A, Matsushima C, Doi RH, Ueda M - Microb Biotechnol (2011)

Bottom Line: As a result, the genome size of C. cellulovorans was about 1 Mbp larger than that of other cellulosome-producing clostridia, mesophilic C. cellulolyticum and thermophilic C. thermocellum.A total of 57 cellulosomal genes were found in the C. cellulovorans genome, and they coded for not only carbohydrate-degrading enzymes but also a lipase, peptidases and proteinase inhibitors.Interestingly, two novel genes encoding scaffolding proteins were found in the genome.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Science, Mie University Graduate School of Bioresources, 1577 Kurimamachiya, Tsu, Mie 514-8507, Japan. ytamaru@bio.mie-u.ac.jp

ABSTRACT
Clostridium cellulovorans, an anaerobic and mesophilic bacterium, degrades native substrates in soft biomass such as corn fibre and rice straw efficiently by producing an extracellular enzyme complex called the cellulosome. Recently, we have reported the whole-genome sequence of C. cellulovorans comprising 4220 predicted genes in 5.10 Mbp [Y. Tamaru et al., (2010) J. Bacteriol., 192: 901–902]. As a result, the genome size of C. cellulovorans was about 1 Mbp larger than that of other cellulosome-producing clostridia, mesophilic C. cellulolyticum and thermophilic C. thermocellum. A total of 57 cellulosomal genes were found in the C. cellulovorans genome, and they coded for not only carbohydrate-degrading enzymes but also a lipase, peptidases and proteinase inhibitors. Interestingly, two novel genes encoding scaffolding proteins were found in the genome. According to KEGG metabolic pathways and their comparison with 11 Clostridial genomes, gene expansion in the C. cellulovorans genome indicated mainly non-cellulosomal genes encoding hemicellulases and pectin-degrading enzymes. Thus, by examining genome sequences from multiple Clostridium species, comparative genomics offers new insight into genome evolution and the way natural selection moulds functional DNA sequence evolution. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced cellulosome-producing Clostridium strains for industrial applications such as biofuel production.

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Cellulosome‐related gene clusters in the C. cellulovorans genome.
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f1: Cellulosome‐related gene clusters in the C. cellulovorans genome.

Mentions: Cellulosomal genes among clostridial genomes were identified and classified as cohesin‐containing scaffolding proteins and dockerin‐containing proteins. So far, the scaffolding proteins for constructing cellulosomes were found in C. acetobutylicum (Sabathe et al., 2002), C. cellulolyticum (Pagès et al., 1999), C. cellulovorans (Shoseyov et al., 1992), C. josui (Kakiuchi et al., 1998) and C. thermocellum (Gerngross et al., 1993). In the case of the C. cellulovorans genome, a total of 57 cellulosomal genes were found, which consisted of 53 dockerin‐containing proteins and four cohesin‐containing scaffolding proteins (Table 2). Two scaffolding proteins, CbpB and CbpC, consisting of a carbohydrate‐binding module (CBM) of family 3, a surface–layer homology domain and a cohesin domain, were newly found and tandemly localized in the C. cellulovorans genome (Fig. 1), while there were no such scaffolding proteins in other cellulosomal clostridia.


Comparison of the mesophilic cellulosome-producing Clostridium cellulovorans genome with other cellulosome-related clostridial genomes.

Tamaru Y, Miyake H, Kuroda K, Nakanishi A, Matsushima C, Doi RH, Ueda M - Microb Biotechnol (2011)

Cellulosome‐related gene clusters in the C. cellulovorans genome.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815796&req=5

f1: Cellulosome‐related gene clusters in the C. cellulovorans genome.
Mentions: Cellulosomal genes among clostridial genomes were identified and classified as cohesin‐containing scaffolding proteins and dockerin‐containing proteins. So far, the scaffolding proteins for constructing cellulosomes were found in C. acetobutylicum (Sabathe et al., 2002), C. cellulolyticum (Pagès et al., 1999), C. cellulovorans (Shoseyov et al., 1992), C. josui (Kakiuchi et al., 1998) and C. thermocellum (Gerngross et al., 1993). In the case of the C. cellulovorans genome, a total of 57 cellulosomal genes were found, which consisted of 53 dockerin‐containing proteins and four cohesin‐containing scaffolding proteins (Table 2). Two scaffolding proteins, CbpB and CbpC, consisting of a carbohydrate‐binding module (CBM) of family 3, a surface–layer homology domain and a cohesin domain, were newly found and tandemly localized in the C. cellulovorans genome (Fig. 1), while there were no such scaffolding proteins in other cellulosomal clostridia.

Bottom Line: As a result, the genome size of C. cellulovorans was about 1 Mbp larger than that of other cellulosome-producing clostridia, mesophilic C. cellulolyticum and thermophilic C. thermocellum.A total of 57 cellulosomal genes were found in the C. cellulovorans genome, and they coded for not only carbohydrate-degrading enzymes but also a lipase, peptidases and proteinase inhibitors.Interestingly, two novel genes encoding scaffolding proteins were found in the genome.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Science, Mie University Graduate School of Bioresources, 1577 Kurimamachiya, Tsu, Mie 514-8507, Japan. ytamaru@bio.mie-u.ac.jp

ABSTRACT
Clostridium cellulovorans, an anaerobic and mesophilic bacterium, degrades native substrates in soft biomass such as corn fibre and rice straw efficiently by producing an extracellular enzyme complex called the cellulosome. Recently, we have reported the whole-genome sequence of C. cellulovorans comprising 4220 predicted genes in 5.10 Mbp [Y. Tamaru et al., (2010) J. Bacteriol., 192: 901–902]. As a result, the genome size of C. cellulovorans was about 1 Mbp larger than that of other cellulosome-producing clostridia, mesophilic C. cellulolyticum and thermophilic C. thermocellum. A total of 57 cellulosomal genes were found in the C. cellulovorans genome, and they coded for not only carbohydrate-degrading enzymes but also a lipase, peptidases and proteinase inhibitors. Interestingly, two novel genes encoding scaffolding proteins were found in the genome. According to KEGG metabolic pathways and their comparison with 11 Clostridial genomes, gene expansion in the C. cellulovorans genome indicated mainly non-cellulosomal genes encoding hemicellulases and pectin-degrading enzymes. Thus, by examining genome sequences from multiple Clostridium species, comparative genomics offers new insight into genome evolution and the way natural selection moulds functional DNA sequence evolution. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced cellulosome-producing Clostridium strains for industrial applications such as biofuel production.

Show MeSH
Related in: MedlinePlus