Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium
The cellulosome of Ruminiclostridium thermocellum was one of the most efficient cellulase systems in nature. However, the product of cellulose degradation by R. thermocellum is cellobiose, which leads to the feedback inhibition of cellulosome, and it limits the R. thermocellum application in the fie...
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1079279/full |
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| author | Sheng Tao Meng Qingbin Li Zhiling Sun Caiyu Li Lixin Liu Lilai |
| author_facet | Sheng Tao Meng Qingbin Li Zhiling Sun Caiyu Li Lixin Liu Lilai |
| author_sort | Sheng Tao |
| collection | DOAJ |
| description | The cellulosome of Ruminiclostridium thermocellum was one of the most efficient cellulase systems in nature. However, the product of cellulose degradation by R. thermocellum is cellobiose, which leads to the feedback inhibition of cellulosome, and it limits the R. thermocellum application in the field of cellulosic biomass consolidated bioprocessing (CBP) industry. In a previous study, R. thermocellum M3, which can hydrolyze cellulosic feedstocks into monosaccharides, was isolated from horse manure. In this study, the complete genome of R. thermocellum M3 was sequenced and assembled. The genome of R. thermocellum M3 was compared with the other R. thermocellum to reveal the mechanism of cellulosic saccharification by R. thermocellum M3. In addition, we predicted the key genes for the elimination of feedback inhibition of cellobiose in R. thermocellum. The results indicated that the whole genome sequence of R. thermocellum M3 consisted of 3.6 Mb of chromosomes with a 38.9% of GC%. To be specific, eight gene islands and 271 carbohydrate-active enzyme-encoded proteins were detected. Moreover, the results of gene function annotation showed that 2,071, 2,120, and 1,246 genes were annotated into the Clusters of Orthologous Groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively, and most of the genes were involved in carbohydrate metabolism and enzymatic catalysis. Different from other R. thermocellum, strain M3 has three proteins related to β-glucosidase, and the cellobiose hydrolysis was enhanced by the synergy of gene BglA and BglX. Meanwhile, the GH42 family, CBM36 family, and AA8 family might participate in cellobiose degradation. |
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| last_indexed | 2024-04-11T00:38:13Z |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-82f562c9aaeb42e1afd445c14ec845802023-01-06T13:34:26ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-01-011310.3389/fmicb.2022.10792791079279Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacteriumSheng Tao0Meng Qingbin1Li Zhiling2Sun Caiyu3Li Lixin4Liu Lilai5College of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, ChinaCollege of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, ChinaState Key Lab of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, ChinaCollege of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, ChinaCollege of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, ChinaCollege of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, ChinaThe cellulosome of Ruminiclostridium thermocellum was one of the most efficient cellulase systems in nature. However, the product of cellulose degradation by R. thermocellum is cellobiose, which leads to the feedback inhibition of cellulosome, and it limits the R. thermocellum application in the field of cellulosic biomass consolidated bioprocessing (CBP) industry. In a previous study, R. thermocellum M3, which can hydrolyze cellulosic feedstocks into monosaccharides, was isolated from horse manure. In this study, the complete genome of R. thermocellum M3 was sequenced and assembled. The genome of R. thermocellum M3 was compared with the other R. thermocellum to reveal the mechanism of cellulosic saccharification by R. thermocellum M3. In addition, we predicted the key genes for the elimination of feedback inhibition of cellobiose in R. thermocellum. The results indicated that the whole genome sequence of R. thermocellum M3 consisted of 3.6 Mb of chromosomes with a 38.9% of GC%. To be specific, eight gene islands and 271 carbohydrate-active enzyme-encoded proteins were detected. Moreover, the results of gene function annotation showed that 2,071, 2,120, and 1,246 genes were annotated into the Clusters of Orthologous Groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively, and most of the genes were involved in carbohydrate metabolism and enzymatic catalysis. Different from other R. thermocellum, strain M3 has three proteins related to β-glucosidase, and the cellobiose hydrolysis was enhanced by the synergy of gene BglA and BglX. Meanwhile, the GH42 family, CBM36 family, and AA8 family might participate in cellobiose degradation.https://www.frontiersin.org/articles/10.3389/fmicb.2022.1079279/fullthermocellumgenomecellobioseβ-glucosidaseCAZyme |
| spellingShingle | Sheng Tao Meng Qingbin Li Zhiling Sun Caiyu Li Lixin Liu Lilai Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium Frontiers in Microbiology thermocellum genome cellobiose β-glucosidase CAZyme |
| title | Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium |
| title_full | Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium |
| title_fullStr | Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium |
| title_full_unstemmed | Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium |
| title_short | Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium |
| title_sort | comparative genomics reveals cellobiose hydrolysis mechanism of ruminiclostridium thermocellum m3 a cellulosic saccharification bacterium |
| topic | thermocellum genome cellobiose β-glucosidase CAZyme |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1079279/full |
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