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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 genome of mesophilic clostridia.
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f2: Cellulosome‐related gene clusters in the genome of mesophilic clostridia.

Mentions: So far, it has been reported that 16S rDNA analysis of phylogenetic diversity among the polysaccharolytic clostridia revealed that C. cellulovorans belonged to cluster I while the other group includes cellulosome‐producing Clostridium species, i.e. C. cellulolyticum and C. thermocellum (Rainey and Stackebrandt, 1993). On the other hand, since the scaffolding protein CipA in C. acetobutylicum is a pseudogene, this bacterium does not produce cellulosomes. The genome sequence in C. cellulovorans was not similar to that in cellulosomal clostridia but was similar to other Clostridium species. Although it has been reported that cellulosomal gene clusters were non‐randomly distributed among mesophilic clostridia, there were several gene clusters containing two or three cellulosomal subunits in the C. cellulovorans genome (Fig. 1). Moreover, cellulosomal gene clusters were conserved only in mesophilic clostridia (Bayer et al., 2008; Doi, 2008). Furthermore, these cellulosomal genes were randomly distributed in the C. cellulovorans genome except for the cellulosomal genes related to a large cellulosomal cluster, whereas two large cellulosomal gene clusters were found in the C. cellulolyticum genome (Fig. 2). Even though the organization of genes encoding cellulosome subunits differs among mesophilic cellulolytic clostridia, there is nonetheless a clear similarity, particularly when looking at the cluster of genes following the main scaffoldin gene. Such a cluster is not found in C. thermocellum. This would suggest that the cellulosomes of the mesophilic clostridia, including the ‘ghost’ cellulosome of C. acetobutylicum, may have arisen from a common ancestral gene cluster. Such a cluster may have been transferred horizontally to C. cellulovorans, since its 16S RNA sequence puts it on a branch different from that harbouring C. cellulolyticum, whereas C. thermocellum, whose 16S RNA is more closely related to that of C. cellulolyticum, has its polysaccharidase genes organized quite differently.


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 genome of mesophilic clostridia.
© Copyright Policy
Related In: Results  -  Collection

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

f2: Cellulosome‐related gene clusters in the genome of mesophilic clostridia.
Mentions: So far, it has been reported that 16S rDNA analysis of phylogenetic diversity among the polysaccharolytic clostridia revealed that C. cellulovorans belonged to cluster I while the other group includes cellulosome‐producing Clostridium species, i.e. C. cellulolyticum and C. thermocellum (Rainey and Stackebrandt, 1993). On the other hand, since the scaffolding protein CipA in C. acetobutylicum is a pseudogene, this bacterium does not produce cellulosomes. The genome sequence in C. cellulovorans was not similar to that in cellulosomal clostridia but was similar to other Clostridium species. Although it has been reported that cellulosomal gene clusters were non‐randomly distributed among mesophilic clostridia, there were several gene clusters containing two or three cellulosomal subunits in the C. cellulovorans genome (Fig. 1). Moreover, cellulosomal gene clusters were conserved only in mesophilic clostridia (Bayer et al., 2008; Doi, 2008). Furthermore, these cellulosomal genes were randomly distributed in the C. cellulovorans genome except for the cellulosomal genes related to a large cellulosomal cluster, whereas two large cellulosomal gene clusters were found in the C. cellulolyticum genome (Fig. 2). Even though the organization of genes encoding cellulosome subunits differs among mesophilic cellulolytic clostridia, there is nonetheless a clear similarity, particularly when looking at the cluster of genes following the main scaffoldin gene. Such a cluster is not found in C. thermocellum. This would suggest that the cellulosomes of the mesophilic clostridia, including the ‘ghost’ cellulosome of C. acetobutylicum, may have arisen from a common ancestral gene cluster. Such a cluster may have been transferred horizontally to C. cellulovorans, since its 16S RNA sequence puts it on a branch different from that harbouring C. cellulolyticum, whereas C. thermocellum, whose 16S RNA is more closely related to that of C. cellulolyticum, has its polysaccharidase genes organized quite differently.

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