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. 2023 Jan 6:13:1079279.
doi: 10.3389/fmicb.2022.1079279. eCollection 2022.

Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium

Sheng Tao  1 , Meng Qingbin  1 , Li Zhiling  2 , Sun Caiyu  1 , Li Lixin  1 , Liu Lilai  1
Affiliations

Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium

Sheng Tao et al. Front Microbiol. .

Abstract

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.

Keywords: CAZyme; cellobiose; genome; thermocellum; β-glucosidase.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Whole-genome visualization map of Ruminiclostridium thermocellum M3.
Figure 2
Figure 2
Venn diagram of core and specific genes among five R. thermocellum strains. Each circle represents an Ruminiclostridium thermocellum strain. The number of orthologous coding sequences (core genome) shared by all strains is shown in the center circle, and the number of specific genes is shown in non-overlapping portions of each oval.
Figure 3
Figure 3
Distribution of core, dispensable, and specific genes on the Clusters of Orthologous Groups (COG) category of Ruminiclostridium thermocellum M3.
Figure 4
Figure 4
Phylogenetic relationship of Ruminiclostridium thermocellum M3 and other four R. thermocellum strains. Numbers along branches indicate bootstrap values with 1,000 times.
Figure 5
Figure 5
Plot of protein linear analysis between Ruminiclostridium thermocellum M3 and other four R. thermocellum.
Figure 6
Figure 6
Phylogenetic tree of β-glucosidase from Ruminiclostridium thermocellum M3. Numbers along branches indicate bootstrap values with 1,000 times.
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