scholarly journals Direct Target Network of the Neurospora crassa Plant Cell Wall Deconstruction Regulators CLR-1, CLR-2, and XLR-1

mBio ◽  
2015 ◽  
Vol 6 (5) ◽  
Author(s):  
James P. Craig ◽  
Samuel T. Coradetti ◽  
Trevor L. Starr ◽  
N. Louise Glass
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Transcription Factors ◽  
Neurospora Crassa ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Nutrient Sensing ◽  
Wall Material ◽  
Content Type ◽  
Genes Encoding

ABSTRACTFungal deconstruction of the plant cell requires a complex orchestration of a wide array of intracellular and extracellular enzymes. InNeurospora crassa, CLR-1, CLR-2, and XLR-1 have been identified as key transcription factors regulating plant cell wall degradation in response to soluble sugars. The XLR-1 regulon was defined using a constitutively active mutant allele, resulting in hemicellulase gene expression and secretion under noninducing conditions. To define genes directly regulated by CLR-1, CLR-2, and XLR-1, we performed chromatin immunoprecipitation and next-generation sequencing (ChIPseq) on epitope-tagged constructs of these three transcription factors. WhenN. crassais exposed to plant cell wall material, CLR-1, CLR-2, and XLR-1 individually bind to the promoters of the most strongly induced genes in their respective regulons. These include promoters of genes encoding cellulases for CLR-1 and CLR-2 (CLR-1/CLR-2) and promoters of genes encoding hemicellulases for XLR-1. CLR-1 bound to its regulon under noninducing conditions; however, this binding alone did not translate into gene expression and enzyme secretion. Motif analysis of the bound genes revealed conserved DNA binding motifs, with the CLR-2 motif matching that of its closest paralog inSaccharomyces cerevisiae, Gal4p. Coimmunoprecipitation studies showed that CLR-1 and CLR-2 act in a homocomplex but not as a CLR-1/CLR-2 heterocomplex.IMPORTANCEUnderstanding fungal regulation of complex plant cell wall deconstruction pathways in response to multiple environmental signals via interconnected transcriptional circuits provides insight into fungus/plant interactions and eukaryotic nutrient sensing. Coordinated optimization of these regulatory networks is likely required for optimal microbial enzyme production.

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.

scholarly journals The Phylogenomic Diversity of Herbivore-AssociatedFibrobacterspp. Is Correlated to Lignocellulose-Degrading Potential

mSphere ◽  
2018 ◽  
Vol 3 (6) ◽  
Author(s):  
Anthony P. Neumann ◽  
Garret Suen
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Phylogenetic Diversity ◽  
Plant Cell Wall ◽  
Carbohydrate Active Enzymes ◽  
Content Type ◽  
Carbohydrate Active Enzyme ◽  
Functional Differences ◽  
Degrading Bacteria ◽  
Genes Encoding

ABSTRACTMembers of the genusFibrobacterare cellulose-degrading bacteria and common constituents of the gastrointestinal microbiota of herbivores. Although considerable phylogenetic diversity is observed among members of this group, few functional differences explaining the distinct ecological distributions of specific phylotypes have been described. In this study, we sequenced and performed a comparative analysis of whole genomes from 38 novelFibrobacterstrains against the type strains for the two formally describedFibrobacterspeciesF. succinogenesstrain S85 andF. intestinalisstrain NR9. Significant differences in the number of genes encoding carbohydrate-active enzyme families involved in plant cell wall polysaccharide degradation were observed amongFibrobacterphylotypes.F. succinogenesgenomes were consistently enriched in genes encoding carbohydrate-active enzymes compared to those ofF. intestinalisstrains. Moreover, genomes ofF. succinogenesphylotypes that are dominant in the rumen had significantly more genes annotated to major families involved in hemicellulose degradation (e.g., CE6, GH10, and GH43) than did the genomes ofF. succinogenesphylotypes typically observed in the lower gut of large hindgut-fermenting herbivores such as horses. Genes encoding a putative urease were also identified in 12 of theFibrobactergenomes, which were primarily isolated from hindgut-fermenting hosts. Screening for growth on urea as the sole source of nitrogen provided strong evidence that the urease was active in these strains. These results represent the strongest evidence reported to date for specific functional differences contributing to the ecology ofFibrobacterspp. in the herbivore gut.IMPORTANCEThe herbivore gut microbiome is incredibly diverse, and a functional understanding of this diversity is needed to more reliably manipulate this community for specific gain, such as increased production in ruminant livestock. Microbial degraders of plant cell wall polysaccharides in the herbivore gut, particularlyFibrobacterspp., are of fundamental importance to their hosts for digestion of a diet consisting primarily of recalcitrant plant fibers. Considerable phylogenetic diversity exists among members of the genusFibrobacter, but much of this diversity remains cryptic. Here, we used comparative genomics, applied to a diverse collection of recently isolatedFibrobacterstrains, to identify a robust association between carbohydrate-active enzyme gene content and theFibrobacterphylogeny. Our results provide the strongest evidence reported to date for functional differences amongFibrobacterphylotypes associated with either the rumen or the hindgut and emphasize the general significance of carbohydrate-active enzymes in the evolution of fiber-degrading bacteria.

scholarly journals Feeding the Walls: How Does Nutrient Availability Regulate Cell Wall Composition?

2018 ◽  
Vol 19 (9) ◽  
pp. 2691 ◽  
Author(s):  
Michael Ogden ◽  
Rainer Hoefgen ◽  
Ute Roessner ◽  
Staffan Persson ◽  
Ghazanfar Khan
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Nutrient Availability ◽  
Cell Walls ◽  
Plant Cell Wall ◽  
Nutrient Status ◽  
Cell Wall Composition ◽  
Nutrient Sensing ◽  
Tissue Type ◽  
Wall Components

Nutrients are critical for plants to grow and develop, and nutrient depletion severely affects crop yield. In order to optimize nutrient acquisition, plants adapt their growth and root architecture. Changes in growth are determined by modifications in the cell walls surrounding every plant cell. The plant cell wall, which is largely composed of complex polysaccharides, is essential for plants to attain their shape and to protect cells against the environment. Within the cell wall, cellulose strands form microfibrils that act as a framework for other wall components, including hemicelluloses, pectins, proteins, and, in some cases, callose, lignin, and suberin. Cell wall composition varies, depending on cell and tissue type. It is governed by synthesis, deposition and remodeling of wall components, and determines the physical and structural properties of the cell wall. How nutrient status affects cell wall synthesis and organization, and thus plant growth and morphology, remains poorly understood. In this review, we aim to summarize and synthesize research on the adaptation of root cell walls in response to nutrient availability and the potential role of cell walls in nutrient sensing.

scholarly journals The Spatio-Temporal Distribution of Cell Wall-Associated Glycoproteins During Wood Formation in Populus

2020 ◽  
Vol 11 ◽  
Author(s):  
Tayebeh Abedi ◽  
Romain Castilleux ◽  
Pieter Nibbering ◽  
Totte Niittylä
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Plant Cell ◽  
Cell Walls ◽  
Plant Cell Wall ◽  
Expression Patterns ◽  
Wood Formation ◽  
Cell Type Specificity ◽  
Spatio Temporal ◽  
Ray Cell

Plant cell wall associated hydroxyproline-rich glycoproteins (HRGPs) are involved in several aspects of plant growth and development, including wood formation in trees. HRGPs such as arabinogalactan-proteins (AGPs), extensins (EXTs), and proline rich proteins (PRPs) are important for the development and architecture of plant cell walls. Analysis of publicly available gene expression data revealed that many HRGP encoding genes show tight spatio-temporal expression patterns in the developing wood of Populus that are indicative of specific functions during wood formation. Similar results were obtained for the expression of glycosyl transferases putatively involved in HRGP glycosylation. In situ immunolabelling of transverse wood sections using AGP and EXT antibodies revealed the cell type specificity of different epitopes. In mature wood AGP epitopes were located in xylem ray cell walls, whereas EXT epitopes were specifically observed between neighboring xylem vessels, and on the ray cell side of the vessel walls, likely in association with pits. Molecular mass and glycan analysis of AGPs and EXTs in phloem/cambium, developing xylem, and mature xylem revealed clear differences in glycan structures and size between the tissues. Separation of AGPs by agarose gel electrophoresis and staining with β-D-glucosyl Yariv confirmed the presence of different AGP populations in phloem/cambium and xylem. These results reveal the diverse changes in HRGP-related processes that occur during wood formation at the gene expression and HRGP glycan biosynthesis levels, and relate HRGPs and glycosylation processes to the developmental processes of wood formation.

scholarly journals Fermentation and subsequent disposition of 14C-labelled plant cell wall material in the rat

1993 ◽  
Vol 69 (1) ◽  
pp. 189-197 ◽  
Author(s):  
D. F. Gray ◽  
M. A. Eastwood ◽  
W. G. Brydon ◽  
S. C. Fry
Keyword(s):  
Cell Wall ◽  
Gastrointestinal Tract ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Spinacia Oleracea ◽  
Wall Material ◽  
Fermentation Products ◽  
Bacterial Fermentation ◽  
Cell Wall Preparation

A 14C-Iabelled plant cell wall preparation (I4C-PCW) produced from spinach (Spinacia oleracea L.) cell culture exhibits uniform labelling of the major polysaccharide groups (%): pectins 53, hemicellulose 13, cellulose 21, starch 3. This 14C-PCW preparation has been used in rat studies as a marker for plant cell wall metabolism. Metabolism of the 14C-PCW occurred largely over the first 24 h. This was due to fermentation in the caecum. The pectic fraction of the plant cell walls was degraded completely in the rat gastrointestinal tract, but some [14C-]cellulose was still detected after 24 h in the colon. Of the 14C,22% was recovered in the host liver, adipose tissue and skin, 26% excreted as 14CO2 and up to 18%was excreted in the faeces. There was no urinary excretion of 14C. In vitro fermentation using a caecal inocuium showed reduced 14CO2 production, 12% compared with 26% in the intact rat. 14C-PCW is auseful marker to investigate the fate of plant cell wall materials in the gastrointestinal tract. These studies show both bacterial fermentation of the 14C-PCW and host metabolism of the 14C-labelled fermentation products.

scholarly journals Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts

PLoS Genetics ◽  
2018 ◽  
Vol 14 (4) ◽  
pp. e1007322 ◽  
Author(s):  
Irina S. Druzhinina ◽  
Komal Chenthamara ◽  
Jian Zhang ◽  
Lea Atanasova ◽  
Dongqing Yang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Lateral Transfer ◽  
Cell Wall Degrading Enzymes ◽  
Degrading Enzymes ◽  
Genes Encoding ◽  
Mycoparasitic Fungus

scholarly journals Glycoside Hydrolase Genes Are Required for Virulence ofAgrobacterium tumefaciensonBryophyllum daigremontianaand Tomato

2019 ◽  
Vol 85 (15) ◽  
Author(s):  
Stephanie L. Mathews ◽  
Haylea Hannah ◽  
Hillary Samagaio ◽  
Camille Martin ◽  
Eleanor Rodriguez-Rassi ◽  
...  
Keyword(s):  
Cell Wall ◽  
Host Cell ◽  
Plant Cell ◽  
Crown Gall ◽  
Plant Cell Wall ◽  
Tumor Formation ◽  
Glycoside Hydrolases ◽  
Plant Host ◽  
Content Type ◽  
Limited Digestion

ABSTRACTAgrobacterium tumefaciensis a rhizosphere bacterium that can infect wound sites on plants. The bacterium transfers a segment of DNA (T-DNA) from the Ti plasmid to the plant host cell via a type IV secretion system where the DNA becomes integrated into the host cell chromosomes. The expression of T-DNA in the plant results in tumor formation. Although the binding of the bacteria to plant surfaces has been studied previously, there is little work on possible interactions of the bacteria with the plant cell wall. Seven of the 48 genes encoding putative glycoside hydrolases (Atu2295,Atu2371,Atu3104,Atu3129,Atu4560,Atu4561, andAtu4665) in the genome ofA. tumefaciensC58 were found to play a role in virulence on tomato andBryophyllum daigremontiana. Two of these genes (pglAandpglB;Atu3129andAtu4560) encode enzymes capable of digesting polygalacturonic acid and, thus, may play a role in the digestion of pectin. One gene (arfA;Atu3104) encodes an arabinosylfuranosidase, which could remove arabinose from the ends of polysaccharide chains. Two genes (bglAandbglB;Atu2295andAtu4561) encode proteins with β-glycosidase activity and could digest a variety of plant cell wall oligosaccharides and polysaccharides. One gene (xynA;Atu2371) encodes a putative xylanase, which may play a role in the digestion of xylan. Another gene (melA;Atu4665) encodes a protein with α-galactosidase activity and may be involved in the breakdown of arabinogalactans. Limited digestion of the plant cell wall byA. tumefaciensmay be involved in tumor formation on tomato andB. daigremontiana.IMPORTANCEA. tumefaciensis used in the construction of genetically engineered plants, as it is able to transfer DNA to plant hosts. Knowledge of the mechanisms of DNA transfer and the genes required will aid in the understanding of this process. Manipulation of glycoside hydrolases may increase transformation and widen the host range of the bacterium.A. tumefaciensalso causes disease (crown gall tumors) on a variety of plants, including stone fruit trees, grapes, and grafted ornamentals such as roses. It is possible that compounds that inhibit glycoside hydrolases could be used to control crown gall disease caused byA. tumefaciens.

scholarly journals Broad Substrate-Specific Phosphorylation Events Are Associated With the Initial Stage of Plant Cell Wall Recognition in Neurospora crassa

2019 ◽  
Vol 10 ◽  
Author(s):  
Maria Augusta C. Horta ◽  
Nils Thieme ◽  
Yuqian Gao ◽  
Kristin E. Burnum-Johnson ◽  
Carrie D. Nicora ◽  
...  
Keyword(s):  
Cell Wall ◽  
Neurospora Crassa ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Initial Stage
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