scholarly journals Network reconstruction and systems analysis of plant cell wall deconstruction byneurospora crassa

2017 ◽  
Author(s):  
Areejit Samal ◽  
James P. Craig ◽  
Samuel T. Coradetti ◽  
J. Philipp Benz ◽  
James A. Eddy ◽  
...  
Keyword(s):  
Cell Wall ◽  
Neurospora Crassa ◽  
Filamentous Fungi ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Plant Biomass ◽  
Degradation Pathway ◽  
Heterogeneous Data ◽  
Data Types ◽  
Cell Wall Polysaccharides

AbstractPlant biomass degradation by fungal derived enzymes is rapidly expanding in economic importance as a clean and efficient source for biofuels. The ability to rationally engineer filamentous fungi would facilitate biotechnological applications for degradation of plant cell wall polysaccharides. However, incomplete knowledge of biomolecular networks responsible for plant cell wall deconstruction impedes experimental efforts in this direction. To expand this knowledge base, a detailed network of reactions important for deconstruction of plant cell wall polysaccharides into simple sugars was constructed for the filamentous fungusNeurospora crassa. To reconstruct this network, information was integrated from five heterogeneous data types: functional genomics, transcriptomics, proteomics, genetics, and biochemical characterizations. The combined information was encapsulated into a feature matrix and the evidence weighed to assign annotation confidence scores for each gene within the network. Comparative analyses of RNA-seq and ChIP-seq data shed light on the regulation of the plant cell wall degradation network (PCWDN), leading to a novel hypothesis for degradation of the hemicellulose mannan. The transcription factor CLR-2 was subsequently experimentally shown to play a key role in the mannan degradation pathway ofNeurospora crassa. Our network serves as a scaffold for integration of diverse experimental data, leading to elucidation of regulatory design principles for plant cell wall deconstruction by filamentous fungi, and guiding efforts to rationally engineer industrially relevant hyper-production strains.

scholarly journals Cryogenian Origin and Subsequent Diversification of the Plant Cell-Wall Enzyme XTH Family

2021 ◽  
Author(s):  
Naoki Shinohara ◽  
Kazuhiko Nishitani
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Evolutionary History ◽  
Plant Cell Wall ◽  
Plant Biomass ◽  
Land Plant ◽  
Cell Wall Polysaccharides ◽  
Fungal Cell ◽  
Considerable Uncertainty ◽  
History Of

Abstract All land plants encode large multigene families of xyloglucan endotransglucosylase/hydrolases (XTHs), plant-specific enzymes that cleave and reconnect plant cell-wall polysaccharides. Despite the ubiquity of these enzymes, considerable uncertainty remains regarding the evolutionary history of the XTH family. Phylogenomic and comparative analyses in this study traced the non-plant origins of the XTH family to Alphaproteobacteria ExoKs, bacterial enzymes involved in loosening biofilms, rather than Firmicutes licheninases, plant biomass digesting enzymes, as previously supposed. The relevant horizontal gene transfer (HGT) event was mapped to the divergence of non-swimming charophycean algae in the Cryogenian geological period. This HGT event was the likely origin of charophycean EG16-2s, which are putative intermediates between ExoKs and XTHs. Another HGT event in the Cryogenian may have led from EG16-2s or ExoKs to fungal CRHs, enzymes that cleave and reconnect chitin and glucans in fungal cell walls. This successive transfer of enzyme-encoding genes may have supported the adaptation of plants and fungi to the ancient icy environment by facilitating their sessile lifestyles. Furthermore, several protein evolutionary steps, including coevolution of substrate-interacting residues and putative intra-family gene fusion, occurred in the land plant lineage and drove diversification of the XTH family. At least some of those events correlated with the evolutionary gain of broader substrate specificities, which may have underpinned the expansion of the XTH family by enhancing duplicated gene survival. Together, this study highlights the Precambrian evolution of life and the mode of multigene family expansion in the evolutionary history of the XTH family.

scholarly journals Identification of Glutaminyl Cyclase Genes Involved in Pyroglutamate Modification of Fungal Lignocellulolytic Enzymes

mBio ◽  
2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Vincent W. Wu ◽  
Craig M. Dana ◽  
Anthony T. Iavarone ◽  
Douglas S. Clark ◽  
N. Louise Glass
Keyword(s):  
Cell Wall ◽  
Neurospora Crassa ◽  
Filamentous Fungi ◽  
Plant Cell ◽  
Mammalian Cells ◽  
Thermal Denaturation ◽  
Plant Cell Wall ◽  
Industrial Plant ◽  
Amino Acid Derivative ◽  
Lignocellulolytic Enzymes

ABSTRACT The breakdown of plant biomass to simple sugars is essential for the production of second-generation biofuels and high-value bioproducts. Currently, enzymes produced from filamentous fungi are used for deconstructing plant cell wall polysaccharides into fermentable sugars for biorefinery applications. A post-translational N-terminal pyroglutamate modification observed in some of these enzymes occurs when N-terminal glutamine or glutamate is cyclized to form a five-membered ring. This modification has been shown to confer resistance to thermal denaturation for CBH-1 and EG-1 cellulases. In mammalian cells, the formation of pyroglutamate is catalyzed by glutaminyl cyclases. Using the model filamentous fungus Neurospora crassa , we identified two genes ( qc - 1 and qc - 2 ) that encode proteins homologous to mammalian glutaminyl cyclases. We show that qc - 1 and qc - 2 are essential for catalyzing the formation of an N-terminal pyroglutamate on CBH-1 and GH5-1. CBH-1 and GH5-1 produced in a Δqc - 1 Δqc - 2 mutant, and thus lacking the N-terminal pyroglutamate modification, showed greater sensitivity to thermal denaturation, and for GH5-1, susceptibility to proteolytic cleavage. QC-1 and QC-2 are endoplasmic reticulum (ER)-localized proteins. The pyroglutamate modification is predicted to occur in a number of additional fungal proteins that have diverse functions. The identification of glutaminyl cyclases in fungi may have implications for production of lignocellulolytic enzymes, heterologous expression, and biotechnological applications revolving around protein stability. IMPORTANCE Pyroglutamate modification is the post-translational conversion of N-terminal glutamine or glutamate into a cyclized amino acid derivative. This modification is well studied in animal systems but poorly explored in fungal systems. In Neurospora crassa , we show that this modification takes place in the ER and is catalyzed by two well-conserved enzymes, ubiquitously conserved throughout the fungal kingdom. We demonstrate that the modification is important for the structural stability and aminopeptidase resistance of CBH-1 and GH5-1, two important cellulase enzymes utilized in industrial plant cell wall deconstruction. Many additional fungal proteins predicted in the genome of N. crassa and other filamentous fungi are predicted to carry an N-terminal pyroglutamate modification. Pyroglutamate addition may also be a useful way to stabilize secreted proteins and peptides, which can be easily produced in fungal production systems.

scholarly journals Plant Cell Wall Hydration and Plant Physiology: An Exploration of the Consequences of Direct Effects of Water Deficit on the Plant Cell Wall

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1263
Author(s):  
David Stuart Thompson ◽  
Azharul Islam
Keyword(s):  
Cell Wall ◽  
Water Content ◽  
Bacterial Cellulose ◽  
Plant Cell ◽  
Cell Walls ◽  
Plant Cell Wall ◽  
Plant Cell Walls ◽  
Cell Wall Polysaccharides ◽  
Degree Of Hydration ◽  
Cellulose Composites

The extensibility of synthetic polymers is routinely modulated by the addition of lower molecular weight spacing molecules known as plasticizers, and there is some evidence that water may have similar effects on plant cell walls. Furthermore, it appears that changes in wall hydration could affect wall behavior to a degree that seems likely to have physiological consequences at water potentials that many plants would experience under field conditions. Osmotica large enough to be excluded from plant cell walls and bacterial cellulose composites with other cell wall polysaccharides were used to alter their water content and to demonstrate that the relationship between water potential and degree of hydration of these materials is affected by their composition. Additionally, it was found that expansins facilitate rehydration of bacterial cellulose and cellulose composites and cause swelling of plant cell wall fragments in suspension and that these responses are also affected by polysaccharide composition. Given these observations, it seems probable that plant environmental responses include measures to regulate cell wall water content or mitigate the consequences of changes in wall hydration and that it may be possible to exploit such mechanisms to improve crop resilience.

scholarly journals PUL-Mediated Plant Cell Wall Polysaccharide Utilization in the Gut Bacteroidetes

2021 ◽  
Vol 22 (6) ◽  
pp. 3077
Author(s):  
Zhenzhen Hao ◽  
Xiaolu Wang ◽  
Haomeng Yang ◽  
Tao Tu ◽  
Jie Zhang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Cell Wall Polysaccharide ◽  
Prominent Feature ◽  
Cell Wall Polysaccharides ◽  
Gut Microbial Community

Plant cell wall polysaccharides (PCWP) are abundantly present in the food of humans and feed of livestock. Mammalians by themselves cannot degrade PCWP but rather depend on microbes resident in the gut intestine for deconstruction. The dominant Bacteroidetes in the gut microbial community are such bacteria with PCWP-degrading ability. The polysaccharide utilization systems (PUL) responsible for PCWP degradation and utilization are a prominent feature of Bacteroidetes. In recent years, there have been tremendous efforts in elucidating how PULs assist Bacteroidetes to assimilate carbon and acquire energy from PCWP. Here, we will review the PUL-mediated plant cell wall polysaccharides utilization in the gut Bacteroidetes focusing on cellulose, xylan, mannan, and pectin utilization and discuss how the mechanisms can be exploited to modulate the gut microbiota.

Formation of Plant Cell Wall Polysaccharides

Nature ◽  
1968 ◽  
Vol 218 (5144) ◽  
pp. 878-880 ◽  
Author(s):  
C. L. VILLEMEZ ◽  
J. M. MCNAB ◽  
P. ALBERSHEIM
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Cell Wall Polysaccharides

Enzymatic Modification of Plant Cell Wall Polysaccharides

2010 ◽  
pp. 367-387 ◽  
Author(s):  
Jens Øbro ◽  
Takahisa Hayashi ◽  
Jørn Dalgaard Mikkelsen
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Enzymatic Modification ◽  
Cell Wall Polysaccharides

scholarly journals Thermophilic Degradation of Hemicellulose, a Critical Feedstock in the Production of Bioenergy and Other Value-Added Products

2020 ◽  
Vol 86 (7) ◽  
Author(s):  
Isaac Cann ◽  
Gabriel V. Pereira ◽  
Ahmed M. Abdel-Hamid ◽  
Heejin Kim ◽  
Daniel Wefers ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Plant Biomass ◽  
Animal Feed ◽  
Value Added ◽  
Building Blocks ◽  
Economic Feasibility ◽  
Renewable Fuels ◽  
Microbial Enzymes

ABSTRACT Renewable fuels have gained importance as the world moves toward diversifying its energy portfolio. A critical step in the biomass-to-bioenergy initiative is deconstruction of plant cell wall polysaccharides to their unit sugars for subsequent fermentation to fuels. To acquire carbon and energy for their metabolic processes, diverse microorganisms have evolved genes encoding enzymes that depolymerize polysaccharides to their carbon/energy-rich building blocks. The microbial enzymes mostly target the energy present in cellulose, hemicellulose, and pectin, three major forms of energy storage in plants. In the effort to develop bioenergy as an alternative to fossil fuel, a common strategy is to harness microbial enzymes to hydrolyze cellulose to glucose for fermentation to fuels. However, the conversion of plant biomass to renewable fuels will require both cellulose and hemicellulose, the two largest components of the plant cell wall, as feedstock to improve economic feasibility. Here, we explore the enzymes and strategies evolved by two well-studied bacteria to depolymerize the hemicelluloses xylan/arabinoxylan and mannan. The sets of enzymes, in addition to their applications in biofuels and value-added chemical production, have utility in animal feed enzymes, a rapidly developing industry with potential to minimize adverse impacts of animal agriculture on the environment.

scholarly journals The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus

2020 ◽  
Vol 117 (11) ◽  
pp. 6003-6013 ◽  
Author(s):  
Vincent W. Wu ◽  
Nils Thieme ◽  
Lori B. Huberman ◽  
Axel Dietschmann ◽  
David J. Kowbel ◽  
...  
Keyword(s):  
Cell Wall ◽  
Transcription Factors ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Plant Biomass ◽  
Carbon Sources ◽  
Cell Wall Degrading Enzymes ◽  
Degrading Enzymes ◽  
Genes Encoding

Filamentous fungi, such asNeurospora crassa, are very efficient in deconstructing plant biomass by the secretion of an arsenal of plant cell wall-degrading enzymes, by remodeling metabolism to accommodate production of secreted enzymes, and by enabling transport and intracellular utilization of plant biomass components. Although a number of enzymes and transcriptional regulators involved in plant biomass utilization have been identified, how filamentous fungi sense and integrate nutritional information encoded in the plant cell wall into a regulatory hierarchy for optimal utilization of complex carbon sources is not understood. Here, we performed transcriptional profiling ofN. crassaon 40 different carbon sources, including plant biomass, to provide data on how fungi sense simple to complex carbohydrates. From these data, we identified regulatory factors inN. crassaand characterized one (PDR-2) associated with pectin utilization and one with pectin/hemicellulose utilization (ARA-1). Using in vitro DNA affinity purification sequencing (DAP-seq), we identified direct targets of transcription factors involved in regulating genes encoding plant cell wall-degrading enzymes. In particular, our data clarified the role of the transcription factor VIB-1 in the regulation of genes encoding plant cell wall-degrading enzymes and nutrient scavenging and revealed a major role of the carbon catabolite repressor CRE-1 in regulating the expression of major facilitator transporter genes. These data contribute to a more complete understanding of cross talk between transcription factors and their target genes, which are involved in regulating nutrient sensing and plant biomass utilization on a global level.

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