Assessing Comparative Microbiome Performance in Plant Cell Wall Deconstruction Using Multi-omics-Informed Network Analysis

Plant cell walls are interwoven structures recalcitrant to degradation. Both native and adapted microbiomes are particularly effective at plant cell wall deconstruction. Studying these deconstructive microbiomes provides an opportunity to assess microbiome performance and relate it to specific microbial populations and enzymes. To establish a system assessing comparative microbiome performance, parallel microbiomes were cultivated on sorghum (Sorghum bicolor L. Moench) from compost inocula. Biomass loss and biochemical assays indicated that these microbiomes diverged in their ability to deconstruct biomass. Network reconstructions from time-dependent gene expression identified key deconstructive groups within the adapted sorghum-degrading communities, including Actinotalea, Filomicrobium, and Gemmanimonadetes populations. Functional analysis of gene expression demonstrated that the microbiomes proceeded through successional stages that are linked to enzymes that deconstruct plant cell wall polymers. This combination of network and functional analysis highlighted the importance of cellulose-active Actinobacteria in differentiating the performance of these microbiomes.

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

Plants ◽

10.3390/plants10071263 ◽

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.

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A Label-free, Fast and High-specificity Technique for Plant Cell Wall Imaging and Composition Analysis

10.21203/rs.3.rs-107437/v1 ◽

2020 ◽

Author(s):

Huimin Xu ◽

Yuanyuan Zhao ◽

Yuanzhen Suo ◽

Yayu Guo ◽

Yi Man ◽

...

Keyword(s):

Cell Wall ◽

Chemical Composition ◽

Raman Scattering ◽

Plant Cell ◽

Cell Walls ◽

Plant Cell Wall ◽

Composition Analysis ◽

Plant Cell Walls ◽

Label Free ◽

Wall Imaging

Abstract Background: Cell wall imaging can considerably permit direct visualization of the molecular architecture of cell walls and provide the detailed chemical information on wall polymers, which is imperative to better exploit and use the biomass polymers; however, detailed imaging and quantifying of the native composition and architecture in the cell wall remains challenging.Results: Here, we describe a label-free imaging technology, coherent Raman scattering microscopy (CRS), including coherent anti-Stokes Raman scattering (CARS) microscopy and stimulated Raman scattering (SRS) microscopy, which images the major structures and chemical composition of plant cell walls. The major steps of the procedure are demonstrated, including sample preparation, setting the mapping parameters, analysis of spectral data, and image generation. Applying this rapid approach, which will help researchers understand the highly heterogeneous structures and organization of plant cell walls.Conclusions: This method can potentially be incorporated into label-free microanalyses of plant cell wall chemical composition based on the in situ vibrations of molecules.

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Plasmodesmata-Related Structural and Functional Proteins: The Long Sought-After Secrets of a Cytoplasmic Channel in Plant Cell Walls

International Journal of Molecular Sciences ◽

10.3390/ijms20122946 ◽

2019 ◽

Vol 20 (12) ◽

pp. 2946 ◽

Cited By ~ 7

Author(s):

Xiao Han ◽

Li-Jun Huang ◽

Dan Feng ◽

Wenhan Jiang ◽

Wenzhuo Miu ◽

...

Keyword(s):

Cell Wall ◽

Plant Cell ◽

Cell Walls ◽

Plasma Membranes ◽

Plant Cell Wall ◽

Plant Cells ◽

Protein Composition ◽

Cell Contact ◽

Plant Cell Walls ◽

Cell Organelles

Plant cells are separated by cellulose cell walls that impede direct cell-to-cell contact. In order to facilitate intercellular communication, plant cells develop unique cell-wall-spanning structures termed plasmodesmata (PD). PD are membranous channels that link the cytoplasm, plasma membranes, and endoplasmic reticulum of adjacent cells to provide cytoplasmic and membrane continuity for molecular trafficking. PD play important roles for the development and physiology of all plants. The structure and function of PD in the plant cell walls are highly dynamic and tightly regulated. Despite their importance, plasmodesmata are among the few plant cell organelles that remain poorly understood. The molecular properties of PD seem largely elusive or speculative. In this review, we firstly describe the general PD structure and its protein composition. We then discuss the recent progress in identification and characterization of PD-associated plant cell-wall proteins that regulate PD function, with particular emphasis on callose metabolizing and binding proteins, and protein kinases targeted to and around PD.

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Plant Cell Wall Changes in Common Wheat Roots as a Result of Their Interaction with Beneficial Fungi of Trichoderma

Cells ◽

10.3390/cells9102319 ◽

2020 ◽

Vol 9 (10) ◽

pp. 2319

Author(s):

Aneta Basińska-Barczak ◽

Lidia Błaszczyk ◽

Kinga Szentner

Keyword(s):

Cell Wall ◽

Common Wheat ◽

Plant Cell ◽

Plant Cell Wall ◽

Arabinogalactan Protein ◽

Plant Cell Walls ◽

Wheat Roots ◽

Wheat Seedlings ◽

Trichoderma Species ◽

Defense Strategies

Plant cell walls play an important role in shaping the defense strategies of plants. This research demonstrates the influence of two differentiators: the lifestyle and properties of the Trichoderma species on cell wall changes in common wheat seedlings. The methodologies used in this investigation include microscopy observations and immunodetection. In this study was shown that the plant cell wall was altered due to its interaction with Trichoderma. The accumulation of lignins and reorganization of pectin were observed. The immunocytochemistry indicated that low methyl-esterified pectins appeared in intercellular spaces. Moreover, it was found that the arabinogalactan protein epitope JIM14 can play a role in the interaction of wheat roots with both the tested Trichoderma strains. Nevertheless, we postulate that modifications, such as the appearance of lignins, rearrangement of low methyl-esterified pectins, and arabinogalactan proteins due to the interaction with Trichoderma show that tested strains can be potentially used in wheat seedlings protection to pathogens.

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

Frontiers in Plant Science ◽

10.3389/fpls.2020.611607 ◽

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.

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

mBio ◽

10.1128/mbio.01452-15 ◽

2015 ◽

Vol 6 (5) ◽

Cited By ~ 53

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.

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ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1) releases latent defense signals in stems with reduced lignin content

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1914422117 ◽

2020 ◽

Vol 117 (6) ◽

pp. 3281-3290 ◽

Cited By ~ 10

Author(s):

Lina Gallego-Giraldo ◽

Chang Liu ◽

Sara Pose-Albacete ◽

Sivakumar Pattathil ◽

Angelo Gabriel Peralta ◽

...

Keyword(s):

Gene Expression ◽

Cell Wall ◽

Plant Cell ◽

Plant Cell Wall ◽

Lignin Content ◽

Ectopic Expression ◽

Cell Wall Degrading Enzymes ◽

Down Regulation ◽

Dehiscence Zone ◽

Cell Wall Remodeling

There is considerable interest in engineering plant cell wall components, particularly lignin, to improve forage quality and biomass properties for processing to fuels and bioproducts. However, modifying lignin content and/or composition in transgenic plants through down-regulation of lignin biosynthetic enzymes can induce expression of defense response genes in the absence of biotic or abiotic stress. Arabidopsis thaliana lines with altered lignin through down-regulation of hydroxycinnamoyl CoA:shikimate/quinate hydroxycinnamoyl transferase (HCT) or loss of function of cinnamoyl CoA reductase 1 (CCR1) express a suite of pathogenesis-related (PR) protein genes. The plants also exhibit extensive cell wall remodeling associated with induction of multiple cell wall-degrading enzymes, a process which renders the corresponding biomass a substrate for growth of the cellulolytic thermophile Caldicellulosiruptor bescii lacking a functional pectinase gene cluster. The cell wall remodeling also results in the release of size- and charge-heterogeneous pectic oligosaccharide elicitors of PR gene expression. Genetic analysis shows that both in planta PR gene expression and release of elicitors are the result of ectopic expression in xylem of the gene ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1), which is normally expressed during anther and silique dehiscence. These data highlight the importance of pectin in cell wall integrity and the value of lignin modification as a tool to interrogate the informational content of plant cell walls.

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Effects of lasalocid and cationomycin on the digestion of plant cell walls in sheep

Canadian Journal of Animal Science ◽

10.4141/cjas91-048 ◽

1991 ◽

Vol 71 (2) ◽

pp. 379-388 ◽

Cited By ~ 9

Author(s):

Catherine Bogaert ◽

L. Gomez ◽

J. P. Jouany

Keyword(s):

Cell Wall ◽

Plant Cell ◽

Cell Walls ◽

Dry Matter ◽

Plant Cell Wall ◽

Control Diet ◽

Nitrogen Concentration ◽

Ammonia Nitrogen ◽

Plant Cell Walls ◽

Flow Measurements

The effect of lasalocid and cationomycin on plant cell wall digestion was tested in a Latin square design experiment over three periods on six adult sheep fed three diets: a control diet (T) without antibiotics, a diet (L) with 33 mg kg−1 of lasalocid, and a diet (C) with 33 mg kg−1 of cationomycin. The dry matter and plant cell wall digestibilities were not affected by the addition of antibiotics. The digestive flow measurements at the duodenum showed that the antibiotic had no effect on the apparent digestion of dry matter, organic matter and plant cell walls along the digestive tract. This was confirmed by the in sacco feed and pure cellulose rumen degradation measurements. Lasalocid, however, decreased the true digestion of feed dry matter in the rumen, as shown by the duodenal flow measurements after being corrected for microbial dry matter. Compared with the control diet, diets (L) and (C) increased the propionate percentage in the rumen VFA mixture (T = 14.9, L = 19.4, C = 18.9) and decreased acetate (T = 66.1, L = 63.8, C = 65.7) and butyrate (T = 14.1, L = 12.7, C = 11.7) percentages. The addition of antibiotics decreased the rumen ammonia nitrogen concentration by 14%. The CO2 to CH4 ratio in the gas mixture was, however, not statistically modified, and no ionophore effect was observed on the protozoa mean population. Key words: Lasalocid, cationomycin, digestion, cell wall carbohydrates, sheep, rumen

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A label-free, fast and high-specificity technique for plant cell wall imaging and composition analysis

Plant Methods ◽

10.1186/s13007-021-00730-9 ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Huimin Xu ◽

Yuanyuan Zhao ◽

Yuanzhen Suo ◽

Yayu Guo ◽

Yi Man ◽

...

Keyword(s):

Cell Wall ◽

Chemical Composition ◽

Raman Scattering ◽

Plant Cell ◽

Cell Walls ◽

Plant Cell Wall ◽

Composition Analysis ◽

Plant Cell Walls ◽

Label Free ◽

Wall Imaging

Abstract Background New cell wall imaging tools permit direct visualization of the molecular architecture of cell walls and provide detailed chemical information on wall polymers, which will aid efforts to use these polymers in multiple applications; however, detailed imaging and quantification of the native composition and architecture in the cell wall remains challenging. Results Here, we describe a label-free imaging technology, coherent Raman scattering (CRS) microscopy, including coherent anti-Stokes Raman scattering (CARS) microscopy and stimulated Raman scattering (SRS) microscopy, which can be used to visualize the major structures and chemical composition of plant cell walls. We outline the major steps of the procedure, including sample preparation, setting the mapping parameters, analysis of spectral data, and image generation. Applying this rapid approach will help researchers understand the highly heterogeneous structures and organization of plant cell walls. Conclusions This method can potentially be incorporated into label-free microanalyses of plant cell wall chemical composition based on the in situ vibrations of molecules.

Download Full-text