Phylogenetic Distribution of Potential Cellulases in Bacteria

ABSTRACTMany microorganisms contain cellulases that are important for plant cell wall degradation and overall soil ecosystem functioning. At present, we have extensive biochemical knowledge of cellulases but little is known about the phylogenetic distribution of these enzymes. To address this, we analyzed the distribution of 21,985 genes encoding proteins related to cellulose utilization in 5,123 sequenced bacterial genomes. First, we identified the distribution of glycoside hydrolases involved in cellulose utilization and synthesis at different taxonomic levels, from the phylum to the strain. Cellulose degradation/utilization capabilities appeared in nearly all major groups and resulted in strains displaying various enzyme gene combinations. Potential cellulose degraders, having both cellulases and β-glucosidases, constituted 24% of all genomes whereas potential opportunistic strains, having β-glucosidases only, accounted for 56%. Finally, 20% of the bacteria have no relevant enzymes and do not rely on cellulose utilization. The latter group was primarily connected to specific bacterial lifestyles like autotrophy and parasitism. Cellulose degraders, as well as opportunists, have multiple enzymes with similar functions. However, the potential degraders systematically harbor about twice more β-glucosidases than their potential opportunistic relatives. Although scattered, the distribution of functional types, in bacterial lineages, is not random but mostly follows a Brownian motion evolution model. Degraders form clusters of relatives at the species level, whereas opportunists are clustered at the genus level. This information can form a mechanistic basis for the linking of changes in microbial community composition to soil ecosystem processes.

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Mechanisms Underlying the Rhizosphere-To-Rhizoplane Enrichment of Cellvibrio Unveiled by Genome-Centric Metagenomics and Metatranscriptomics

Microorganisms ◽

10.3390/microorganisms8040583 ◽

2020 ◽

Vol 8 (4) ◽

pp. 583

Author(s):

Yunzeng Zhang ◽

Jin Xu ◽

Entao Wang ◽

Nian Wang

Keyword(s):

Plant Cell ◽

Cell Walls ◽

Plant Cell Wall ◽

Iron Acquisition ◽

Root Surface ◽

Gene Gain ◽

Plant Cell Walls ◽

Genes Encoding ◽

Enhanced Expression ◽

Plant Cell Wall Degradation

Maintaining integrity of the plant cell walls is critical for plant health, however, our previous study showed that Cellvibrio, which is recognized by its robust ability to degrade plant cell walls, was enriched from the citrus rhizosphere to the rhizoplane (i.e., the root surface). Here we investigated the mechanisms underlying the rhizosphere-to-rhizoplane enrichment of Cellvibrio through genome-centric metagenomics and metatranscriptomics analyses. We recovered a near-complete metagenome-assembled genome representing a potentially novel species of Cellvibrio, herein designated Bin79, with genome size of 5.71 Mb across 11 scaffolds. Differential gene expression analysis demonstrated that plant cell wall degradation genes were repressed, whereas genes encoding chitin-degrading enzymes were induced in the rhizoplane compared with the rhizosphere. Enhanced expression of multi-drug efflux genes and iron acquisition- and storage-associated genes in the rhizoplane indicated mechanisms by which Bin79 competes with other microbes. In addition, genes involved in repelling plant immune responses were significantly activated in the rhizoplane. Comparative genomics analyses with five related Cellvibrio strains showed the importance of gene gain events for the rhizoplane adaptation of Bin79. Overall, this study characterizes a novel Cellvibrio strain and indicates the mechanisms involved in its adaptation to the rhizoplane from meta-omics data without cultivation.

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Genomic Potential for Polysaccharide Deconstruction in Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.03718-14 ◽

2014 ◽

Vol 81 (4) ◽

pp. 1513-1519 ◽

Cited By ~ 73

Author(s):

Renaud Berlemont ◽

Adam C. Martiny

Keyword(s):

Microbial Communities ◽

Bacterial Growth ◽

Glycoside Hydrolase ◽

Glycoside Hydrolases ◽

Phylogenetic Distribution ◽

Bacterial Genomes ◽

Oligosaccharide Processing ◽

Taxonomic Groups ◽

Structural Polymers

ABSTRACTGlycoside hydrolases are important enzymes that support bacterial growth by enabling the degradation of polysaccharides (e.g., starch, cellulose, xylan, and chitin) in the environment. Presently, little is known about the overall phylogenetic distribution of the genomic potential to degrade these polysaccharides in bacteria. However, knowing the phylogenetic breadth of these traits may help us predict the overall polysaccharide processing in environmental microbial communities. In order to address this, we identified and analyzed the distribution of 392,166 enzyme genes derived from 53 glycoside hydrolase families in 8,133 sequenced bacterial genomes. Enzymes for oligosaccharides and starch/glycogen were observed in most taxonomic groups, whereas glycoside hydrolases for structural polymers (i.e., cellulose, xylan, and chitin) were observed in clusters of relatives at taxonomic levels ranging from species to genus as determined by consenTRAIT. The potential for starch and glycogen processing, as well as oligosaccharide processing, was observed in 85% of the strains, whereas 65% possessed enzymes to degrade some structural polysaccharides (i.e., cellulose, xylan, or chitin). Potential degraders targeting one, two, and three structural polysaccharides accounted for 22.6, 32.9, and 9.3% of genomes analyzed, respectively. Finally, potential degraders targeting multiple structural polysaccharides displayed increased potential for oligosaccharide deconstruction. This study provides a framework for linking the potential for polymer deconstruction with phylogeny in complex microbial assemblages.

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High Potential Source for Biomass Degradation Enzyme Discovery and Environmental Aspects Revealed through Metagenomics of Indian Buffalo Rumen

BioMed Research International ◽

10.1155/2014/267189 ◽

2014 ◽

Vol 2014 ◽

pp. 1-10 ◽

Cited By ~ 18

Author(s):

K. M. Singh ◽

Bhaskar Reddy ◽

Dishita Patel ◽

A. K. Patel ◽

Nidhi Parmar ◽

...

Keyword(s):

Plant Cell Wall ◽

Glycoside Hydrolases ◽

Carbohydrate Binding ◽

Metagenomic Sequencing ◽

Environmental Aspects ◽

Rumen Microbiome ◽

Polysaccharide Lyases ◽

Effective System ◽

Plant Cell Wall Degradation ◽

Buffalo Rumen

The complex microbiomes of the rumen functions as an effective system for plant cell wall degradation, and biomass utilization provide genetic resource for degrading microbial enzymes that could be used in the production of biofuel. Therefore the buffalo rumen microbiota was surveyed using shot gun sequencing. This metagenomic sequencing generated 3.9 GB of sequences and data were assembled into 137270 contiguous sequences (contigs). We identified potential 2614 contigs encoding biomass degrading enzymes including glycoside hydrolases (GH: 1943 contigs), carbohydrate binding module (CBM: 23 contigs), glycosyl transferase (GT: 373 contigs), carbohydrate esterases (CE: 259 contigs), and polysaccharide lyases (PE: 16 contigs). The hierarchical clustering of buffalo metagenomes demonstrated the similarities and dissimilarity in microbial community structures and functional capacity. This demonstrates that buffalo rumen microbiome was considerably enriched in functional genes involved in polysaccharide degradation with great prospects to obtain new molecules that may be applied in the biofuel industry.

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Molecular Analysis of Cellulosome Organization in Ruminococcus Albus and Fibrobacter Intestinalis for Optimization of Fiber Digestibility in Ruminants

10.32747/2004.7586475.bard ◽

2004 ◽

Author(s):

Mark Morrison ◽

Joshuah Miron ◽

Edward A. Bayer ◽

Raphael Lamed

Keyword(s):

Plant Cell Wall ◽

Cellulose Degradation ◽

Structural Features ◽

Glycoside Hydrolases ◽

Carbohydrate Binding ◽

Cellulolytic Bacteria ◽

Modular Architecture ◽

Host Animal ◽

Ruminococcus Albus ◽

Fiber Degradation

Improving plant cell wall (fiber) degradation remains one of the highest priority research goals for all ruminant enterprises dependent on forages, hay, silage, or other fibrous byproducts as energy sources, because it governs the provision of energy-yielding nutrients to the host animal. Although the predominant species of microbes responsible for ruminal fiber degradation are culturable, the enzymology and genetics underpinning the process are poorly defined. In that context, there were two broad objectives for this proposal. The first objective was to identify the key cellulosomal components in Ruminococcus albus and to characterize their structural features as well as regulation of their expression, in response to polysaccharides and (or) P AA/PPA. The second objective was to evaluate the similarities in the structure and architecture of cellulosomal components between R. albus and other ruminal and non-ruminal cellulolytic bacteria. The cooperation among the investigators resulted in the identification of two glycoside hydrolases rate-limiting to cellulose degradation by Ruminococcus albus (Cel48A and CeI9B) and our demonstration that these enzymes possess a novel modular architecture specific to this bacterium (Devillard et al. 2004). We have now shown that the novel X-domains in Cel48A and Cel9B represent a new type of carbohydrate binding module, and the enzymes are not part of a ceiluiosome-like complex (CBM37, Xu et al. 2004). Both Cel48A and Cel9B are conditionally expressed in response to P AA/PPA, explaining why cellulose degradation in this bacterium is affected by the availability of these compounds, but additional studies have shown for the first time that neither PAA nor PPA influence xylan degradation by R. albus (Reveneau et al. 2003). Additionally, the R. albus genome sequencing project, led by the PI. Morrison, has supported our identification of many dockerin containing proteins. However, the identification of gene(s) encoding a scaffoldin has been more elusive, and recombinant proteins encoding candidate cohesin modules are now being used in Israel to verify the existence of dockerin-cohesin interactions and cellulosome production by R. albus. The Israeli partners have also conducted virtually all of the studies specific to the second Objective of the proposal. Comparative blotting studies have been conducted using specific antibodies prepare against purified recombinant cohesins and X-domains, derived from cellulosomal scaffoldins of R. flavefaciens 17, a Clostridium thermocellum mutant-preabsorbed antibody preparation, or against CbpC (fimbrial protein) of R. albus 8. The data also suggest that additional cellulolytic bacteria including Fibrobacter succinogenes S85, F. intestinalis DR7 and Butyrivibrio fibrisolvens Dl may also employ cellulosomal modules similar to those of R. flavefaciens 17. Collectively, our work during the grant period has shown that R. albus and other ruminal bacteria employ several novel mechanisms for their adhesion to plant surfaces, and produce both cellulosomal and non-cellulosomal forms of glycoside hydrolases underpinning plant fiber degradation. These improvements in our mechanistic understanding of bacterial adhesion and enzyme regulation now offers the potential to: i) optimize ruminal and hindgut conditions by dietary additives to maximize fiber degradation (e.g. by the addition of select enzymes or PAA/PPA); ii) identify plant-borne influences on adhesion and fiber-degradation, which might be overcome (or improved) by conventional breeding or transgenic plant technologies and; iii) engineer or select microbes with improved adhesion capabilities, cellulosome assembly and fiber degradation. The potential benefits associated with this research proposal are likely to be realized in the medium term (5-10 years).

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DIPG-41. DISSECTING THE MECHANISTIC BASIS FOR ACVR1 AND PIK3CA MUTATION CO-OCCURRENCE IN DIFFUSE MIDLINE GLIOMAS USING GENETICALLY ENGINEERED MOUSE MODELS

Neuro-Oncology ◽

10.1093/neuonc/noaa222.088 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii295-iii295

Author(s):

Annette Wu ◽

Tak Mak ◽

Jerome Fortin

Keyword(s):

Mouse Models ◽

Pik3ca Mutation ◽

Cell Lineage ◽

Gene Expression Signature ◽

Genetically Engineered ◽

Genetically Engineered Mouse Models ◽

Dismal Prognosis ◽

Human Pathology ◽

Genes Encoding ◽

Mechanistic Basis

Abstract Diffuse midline gliomas (DMGs) are aggressive childhood brain tumors with a dismal prognosis. Most of these tumors carry K27M mutations in histone H3-encoding genes, particularly H3F3A and HIST1H3B. In addition, activating mutations in ACVR1 and PIK3CA co-occur in a subset of DMGs. To understand how these lesions drive the development of DMGs, we generated genetically engineered mouse models in which Acvr1G328V, Hist1h3bK27M, and Pik3caH1047R are targeted to the OLIG2-expressing cell lineage. Animals carrying Acvr1G328V and Pik3caH1047R, with (“AHPO”) or without (“APO”) Hist1h3bK27M, developed high-grade diffuse gliomas involving midline and forebrain regions. Neither Acvr1G328V nor Pik3caH1047R drove tumorigenesis by themselves, but Acvr1G328V was sufficient to cause oligodendroglial differentiation arrest, pointing to a role in the earliest stages of gliomas formation. Transcriptomic analyses of AHPO and APO tumors indicated a predominantly proneural and oligodendrocyte precursor-like gene expression signature, consistent with the corresponding human pathology. Genes encoding transcription factors (TFs) with dual roles in controlling glial and neuronal differentiation were upregulated in tumors. Some of these genes were mildly induced by Acvr1G328V alone. Functional experiments using CRISPR/Cas9-mediated gene editing in patient-derived cell lines confirmed a role for some of these TFs in controlling DMG cell fitness. Overall, our results suggest that Pik3caH1047R consolidates Acvr1G328V-induced glial differentiation arrest to drive DMG development and progression.

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Discovery of LPMO activity on hemicelluloses shows the importance of oxidative processes in plant cell wall degradation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1323629111 ◽

2014 ◽

Vol 111 (17) ◽

pp. 6287-6292 ◽

Cited By ~ 227

Author(s):

J. W. Agger ◽

T. Isaksen ◽

A. Varnai ◽

S. Vidal-Melgosa ◽

W. G. T. Willats ◽

...

Keyword(s):

Cell Wall ◽

Plant Cell ◽

Plant Cell Wall ◽

Cell Wall Degradation ◽

Oxidative Processes ◽

Plant Cell Wall Degradation

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Analysis of saponins detoxification genes in Ilyonectria mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

Archives of Microbiology ◽

10.1007/s00203-021-02502-4 ◽

2021 ◽

Author(s):

Guohong Zeng ◽

Jin Li ◽

Yuxiu Ma ◽

Qian Pu ◽

Tian Xiao ◽

...

Keyword(s):

Root Rot ◽

Molecular Mechanisms ◽

Management Strategies ◽

Panax Notoginseng ◽

Glycoside Hydrolases ◽

Rna Seq ◽

Host Interaction ◽

Excellent Starting Point ◽

Starting Point ◽

Genes Encoding

AbstractSaponins are kinds of antifungal compounds produced by Panax notoginseng to resist invasion by pathogens. Ilyonectria mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4H (Hours) and 12H (Hours) compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4H and 12H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation–reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen–Host Interaction) genes out of those 93 up-regulated genes. In this report, we analyzed virulence-associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

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Genome Sequence of the Polysaccharide-Degrading, Thermophilic Anaerobe Spirochaeta thermophila DSM 6192

Journal of Bacteriology ◽

10.1128/jb.01023-10 ◽

2010 ◽

Vol 192 (24) ◽

pp. 6492-6493 ◽

Cited By ~ 13

Author(s):

Angel Angelov ◽

Susanne Liebl ◽

Meike Ballschmiter ◽

Mechthild Bömeke ◽

Rüdiger Lehmann ◽

...

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Glycoside Hydrolase ◽

Enzyme System ◽

Cellulose Degradation ◽

Carbohydrate Binding ◽

Carbohydrate Binding Module ◽

Free Living ◽

Genome Data ◽

Genes Encoding

ABSTRACT Spirochaeta thermophila is a thermophilic, free-living anaerobe that is able to degrade various α- and β-linked sugar polymers, including cellulose. We report here the complete genome sequence of S. thermophila DSM 6192, which is the first genome sequence of a thermophilic, free-living member of the Spirochaetes phylum. The genome data reveal a high density of genes encoding enzymes from more than 30 glycoside hydrolase families, a noncellulosomal enzyme system for (hemi)cellulose degradation, and indicate the presence of a novel carbohydrate-binding module.

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Random Mutagenesis of Clostridium cellulolyticum by Using a Tn1545 Derivative

Applied and Environmental Microbiology ◽

10.1128/aem.02417-09 ◽

2010 ◽

Vol 76 (13) ◽

pp. 4546-4549 ◽

Cited By ~ 9

Author(s):

Jean-Charles Blouzard ◽

Odile Valette ◽

Chantal Tardif ◽

Pascale de Philip

Keyword(s):

Cell Wall ◽

Metabolic Engineering ◽

Plant Cell ◽

Plant Cell Wall ◽

Random Mutagenesis ◽

Cell Wall Degradation ◽

Clostridium Cellulolyticum ◽

Plant Cell Wall Degradation ◽

Random Insertion

ABSTRACT Further understanding of the plant cell wall degradation system of Clostridium cellulolyticum and the possibility of metabolic engineering in this species highlight the need for a means of random mutagenesis. Here, we report the construction of a Tn1545-derived delivery tool which allows monocopy random insertion within the genome.

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Complete Genome Sequence of the Polysaccharide-Degrading Rumen Bacterium Pseudobutyrivibrio xylanivorans MA3014

10.1101/2020.07.08.194233 ◽

2020 ◽

Author(s):

Nikola Palevich ◽

Paul H. Maclean ◽

William J. Kelly ◽

Sinead C. Leahy ◽

Jasna Rakonjac ◽

...

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Bacterial Species ◽

Glycoside Hydrolases ◽

Rumen Bacterium ◽

Protein Coding ◽

Plant Polysaccharides ◽

Plant Matter ◽

Genes Encoding

AbstractRuminants are essential for maintaining the global population and managing greenhouse gas emissions. In the rumen, bacterial species belonging to the genera rumen Butyrivibrio and Pseudobutyrivibrio constitute the core bacterial rumen microbiome and are important degraders of plant-derived complex polysaccharides. Pseudobutyrivibrio xylanivorans MA3014 was selected for genome sequencing in order to examine its ability to breakdown and utilize plant polysaccharides. The complete genome sequence of MA3014 is 3.58 Mb, consists of three replicons (a chromosome, chromid and plasmid), has an overall G+C content of 39.6% and encodes 3,265 putative protein-coding genes (PCGs). Comparative pan-genomics of all cultivated and currently available P. xylanivorans genomes has revealed highly open genomes and a strong correlation of orthologous genes within this species of rumen bacteria. MA3014 is metabolically versatile and capable of utilizing a range of simple mono-or oligosaccharides to complex plant polysaccharides such as pectins, mannans, starch and hemicelluloses for growth, with lactate, butyrate and formate as the principal fermentation end-products. The genes encoding these metabolic pathways have been identified and MA3014 is predicted to encode an extensive repertoire of Carbohydrate-Active enZYmes (CAZymes) with 80 Glycoside Hydrolases (GHs), 28 Carbohydrate Esterases (CEs) and 51 Glycosyl Transferases (GTs), that suggest its role as an initiator of primary solubilization of plant matter in the rumen.

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