scholarly journals Publisher Correction: Deciphering the unique cellulose degradation mechanism of the ruminal bacterium Fibrobacter succinogenes S85

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mahendra P. Raut ◽  
Narciso Couto ◽  
Esther Karunakaran ◽  
Catherine A. Biggs ◽  
Phillip C. Wright
Keyword(s):  
Cellulose Degradation ◽  
Degradation Mechanism ◽  
Fibrobacter Succinogenes ◽  
Ruminal Bacterium

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

scholarly journals Deciphering the unique cellulose degradation mechanism of the ruminal bacterium Fibrobacter succinogenes S85

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mahendra P. Raut ◽  
Narciso Couto ◽  
Esther Karunakaran ◽  
Catherine A. Biggs ◽  
Phillip C. Wright
Keyword(s):  
Cellulose Degradation ◽  
Cell Envelope ◽  
Degradation Mechanism ◽  
Protein Profile ◽  
Lignocellulose Degradation ◽  
Fibrobacter Succinogenes ◽  
Molecular Features ◽  
Associated Proteins ◽  
Lignocellulosic Biofuels ◽  
First Time

Abstract Fibrobacter succinogenes S85, isolated from the rumen of herbivores, is capable of robust lignocellulose degradation. However, the mechanism by which it achieves this is not fully elucidated. In this study, we have undertaken the most comprehensive quantitative proteomic analysis, to date, of the changes in the cell envelope protein profile of F. succinogenes S85 in response to growth on cellulose. Our results indicate that the cell envelope proteome undergoes extensive rearrangements to accommodate the cellulolytic degradation machinery, as well as associated proteins involved in adhesion to cellulose and transport and metabolism of cellulolytic products. Molecular features of the lignocellulolytic enzymes suggest that the Type IX secretion system is involved in the translocation of these enzymes to the cell envelope. Finally, we demonstrate, for the first time, that cyclic-di-GMP may play a role in mediating catabolite repression, thereby facilitating the expression of proteins involved in the adhesion to lignocellulose and subsequent lignocellulose degradation and utilisation. Understanding the fundamental aspects of lignocellulose degradation in F. succinogenes will aid the development of advanced lignocellulosic biofuels.

scholarly journals β-Glucosidase genes differentially expressed during composting

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Xinyue Zhang ◽  
Bo Ma ◽  
Jiawen Liu ◽  
Xiehui Chen ◽  
Shanshan Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Environmental Changes ◽  
Cellulose Degradation ◽  
Degradation Mechanism ◽  
Degradation Process ◽  
Global Scale ◽  
Expression Of Genes ◽  
Glucose Tolerant ◽  
Cooling Phase ◽  
And Function

Abstract Background Cellulose degradation by cellulase is brought about by complex communities of interacting microorganisms, which significantly contribute to the cycling of carbon on a global scale. β-Glucosidase (BGL) is the rate-limiting enzyme in the cellulose degradation process. Thus, analyzing the expression of genes involved in cellulose degradation and regulation of BGL gene expression during composting will improve the understanding of the cellulose degradation mechanism. Based on our previous research, we hypothesized that BGL-producing microbial communities differentially regulate the expression of glucose-tolerant BGL and non-glucose-tolerant BGL to adapt to the changes in cellulose degradation conditions. Results To confirm this hypothesis, the structure and function of functional microbial communities involved in cellulose degradation were investigated by metatranscriptomics and a DNA library search of the GH1 family of BGLs involved in natural and inoculated composting. Under normal conditions, the group of non-glucose-tolerant BGL genes exhibited higher sensitivity to regulation than the glucose-tolerant BGL genes, which was suppressed during the composting process. Compared with the expression of endoglucanase and exoglucanase, the functional microbial communities exhibited a different transcriptional regulation of BGL genes during the cooling phase of natural composting. BGL-producing microbial communities upregulated the expression of glucose-tolerant BGL under carbon catabolite repression due to the increased glucose concentration, whereas the expression of non-glucose-tolerant BGL was suppressed. Conclusion Our results support the hypothesis that the functional microbial communities use multiple strategies of varying effectiveness to regulate the expression of BGL genes to facilitate adaptation to environmental changes.

scholarly journals Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85

PLoS ONE ◽  
2015 ◽  
Vol 10 (12) ◽  
pp. e0143809 ◽  
Author(s):  
Meagan C. Burnet ◽  
Alice C. Dohnalkova ◽  
Anthony P. Neumann ◽  
Mary S. Lipton ◽  
Richard D. Smith ◽  
...  
Keyword(s):  
Cellulose Degradation ◽  
Fibrobacter Succinogenes

A T9SS Substrate Involved in Crystalline Cellulose Degradation by Affecting Crucial Cellulose Binding Proteins in Cytophaga hutchinsonii

2021 ◽  
Author(s):  
Lijuan Gao ◽  
Yaru Su ◽  
Wenxia Song ◽  
Weican Zhang ◽  
Qingsheng Qi ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Gene Locus ◽  
Cellulose Degradation ◽  
Degradation Mechanism ◽  
Crystalline Cellulose ◽  
Cellulolytic Bacterium ◽  
Cytophaga Hutchinsonii ◽  
Surface Localization ◽  
Cell Surface Localization ◽  
Cellulose Binding

Cytophaga hutchinsonii is an abundant soil cellulolytic bacterium that uses a unique cellulose degradation mechanism different from those that involve free cellulases or cellulosomes. Though several proteins were identified to be important for cellulose degradation, the mechanism used by C. hutchinsonii to digest crystalline cellulose remains a mystery. In this study, chu_0922 was identified by insertional mutation and gene deletion as an important gene locus indispensable for crystalline cellulose utilization. Deletion of chu_0922 resulted in defect in crystalline cellulose utilization. The Δ 0922 mutant completely lost the ability to grow on crystalline cellulose even with extended incubation, and selectively utilized the amorphous region of cellulose leading to the increased crystallinity. As a protein secreted by the type Ⅸ secretion system (T9SS), CHU_0922 was found to be located on the outer membrane, and the outer membrane localization of CHU_0922 relied on the T9SS. Comparative analysis of the outer membrane proteins revealed that the abundance of several cellulose binding proteins, including CHU_1276, CHU_1277, and CHU_1279, was reduced in the Δ 0922 mutant. Further study showed that CHU_0922 is crucial for the full expression of the gene cluster containing chu_1276 , chu_1277 , chu_1278 , chu_1279 , and chu_1280 ( cel9C ), which is essential for cellulose utilization. Moreover, CHU_0922 is required for the cell surface localization of CHU_3220, a cellulose binding protein that is essential for crystalline cellulose utilization. Our study provides insights into the complex system that C. hutchinsonii uses to degrade crystalline cellulose. IMPORTANCE The widespread aerobic cellulolytic bacterium Cytophaga hutchinsonii , belonging to the phylum Bacteroidetes , utilizes a novel mechanism to degrade crystalline cellulose. No genes encoding proteins specialized in loosening or disruption the crystalline structure of cellulose were identified in the genome of C. hutchinsonii , except for chu_3220 and chu_1557 . The crystalline cellulose degradation mechanism remains enigmatic. This study identified a new gene locus, chu_0922 , encoding a typical T9SS substrate that is essential for crystalline cellulose degradation. Notably, CHU_0922 is crucial for the normal transcription of chu_1276 , chu_1277 , chu_1278 , chu_1279 , and chu_1280 ( cel9C ), which play important roles in the degradation of cellulose. Moreover, CHU_0922 participates in the cell surface localization of CHU_3220. These results demonstrated that CHU_0922 plays a key role in the crystalline cellulose degradation network. Our study will promote the uncovering of the novel cellulose utilization mechanism of C. hutchinsonii.

scholarly journals Inactivation of Cellobiose Dehydrogenases Modifies the Cellulose Degradation Mechanism of Podospora anserina

2016 ◽  
Vol 83 (2) ◽  
Author(s):  
Narumon Tangthirasunun ◽  
David Navarro ◽  
Sona Garajova ◽  
Didier Chevret ◽  
Laetitia Chan Ho Tong ◽  
...  
Keyword(s):  
Plant Biomass ◽  
Cellulose Degradation ◽  
Degradation Mechanism ◽  
Podospora Anserina ◽  
Cellulosic Biomass ◽  
Striking Difference ◽  
Crystalline Cellulose ◽  
Minor Role ◽  
Wild Type ◽  
Content Type

ABSTRACT Conversion of biomass into high-value products, including biofuels, is of great interest to developing sustainable biorefineries. Fungi are an inexhaustible source of enzymes to degrade plant biomass. Cellobiose dehydrogenases (CDHs) play an important role in the breakdown through synergistic action with fungal lytic polysaccharide monooxygenases (LPMOs). The three CDH genes of the model fungus Podospora anserina were inactivated, resulting in single and multiple CDH mutants. We detected almost no difference in growth and fertility of the mutants on various lignocellulose sources, except on crystalline cellulose, on which a 2-fold decrease in fertility of the mutants lacking P. anserina CDH1 (PaCDH1) and PaCDH2 was observed. A striking difference between wild-type and mutant secretomes was observed. The secretome of the mutant lacking all CDHs contained five beta-glucosidases, whereas the wild type had only one. P. anserina seems to compensate for the lack of CDH with secretion of beta-glucosidases. The addition of P. anserina LPMO to either the wild-type or mutant secretome resulted in improvement of cellulose degradation in both cases, suggesting that other redox partners present in the mutant secretome provided electrons to LPMOs. Overall, the data showed that oxidative degradation of cellulosic biomass relies on different types of mechanisms in fungi. IMPORTANCE Plant biomass degradation by fungi is a complex process involving dozens of enzymes. The roles of each enzyme or enzyme class are not fully understood, and utilization of a model amenable to genetic analysis should increase the comprehension of how fungi cope with highly recalcitrant biomass. Here, we report that the cellobiose dehydrogenases of the model fungus Podospora anserina enable it to consume crystalline cellulose yet seem to play a minor role on actual substrates, such as wood shavings or miscanthus. Analysis of secreted proteins suggests that Podospora anserina compensates for the lack of cellobiose dehydrogenase by increasing beta-glucosidase expression and using an alternate electron donor for LPMO.

scholarly journals FLP-FRT-Based Method To Obtain Unmarked Deletions ofCHU_3237(porU) and Large Genomic Fragments of Cytophaga hutchinsonii

2014 ◽  
Vol 80 (19) ◽  
pp. 6037-6045 ◽  
Author(s):  
Ying Wang ◽  
Zhiquan Wang ◽  
Jing Cao ◽  
Zhiwei Guan ◽  
Xuemei Lu
Keyword(s):  
Cellulose Degradation ◽  
Degradation Mechanism ◽  
Signal Peptidase ◽  
Crystalline Cellulose ◽  
Cellulolytic Bacterium ◽  
Efficient Tool ◽  
Content Type ◽  
Cytophaga Hutchinsonii ◽  
Recombination System ◽  
Colony Spreading

ABSTRACTCytophaga hutchinsoniiis a widely distributed cellulolytic bacterium in the phylumBacteroidetes. It can digest crystalline cellulose rapidly without free cellulases or cellulosomes. The mechanism of its cellulose utilization remains a mystery. We developed an efficient method based on a linear DNA double-crossover and FLP-FRT recombination system to obtain unmarked deletions of both single genes and large genomic fragments inC. hutchinsonii. Unmarked deletion ofCHU_3237(porU), an ortholog of the C-terminal signal peptidase of a type IX secretion system (T9SS), resulted in defects in colony spreading, cellulose degradation, and protein secretion, indicating that it is a component of the T9SS and that T9SS plays an important role in cellulose degradation byC. hutchinsonii. Furthermore, deletions of four large genomic fragments were obtained using our method, and the sizes of the excised fragments varied from 9 to 19 kb, spanning from 6 to 22 genes. The customized FLP-FRT method provides an efficient tool for more rapid progress in the cellulose degradation mechanism and other physiological aspects ofC. hutchinsonii.

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