scholarly journals Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jeffrey P. Tingley ◽  
Kristin E. Low ◽  
Xiaohui Xing ◽  
D. Wade Abbott
Keyword(s):  
Cell Wall ◽  
Microbial Communities ◽  
Cell Walls ◽  
Crop Residues ◽  
Monosaccharide Composition ◽  
Wall Structure ◽  
Agricultural Crop ◽  
Fine Chemistry ◽  
Fermentable Carbohydrates

AbstractThe production of biofuels as an efficient source of renewable energy has received considerable attention due to increasing energy demands and regulatory incentives to reduce greenhouse gas emissions. Second-generation biofuel feedstocks, including agricultural crop residues generated on-farm during annual harvests, are abundant, inexpensive, and sustainable. Unlike first-generation feedstocks, which are enriched in easily fermentable carbohydrates, crop residue cell walls are highly resistant to saccharification, fermentation, and valorization. Crop residues contain recalcitrant polysaccharides, including cellulose, hemicelluloses, pectins, and lignin and lignin-carbohydrate complexes. In addition, their cell walls can vary in linkage structure and monosaccharide composition between plant sources. Characterization of total cell wall structure, including high-resolution analyses of saccharide composition, linkage, and complex structures using chromatography-based methods, nuclear magnetic resonance, -omics, and antibody glycome profiling, provides critical insight into the fine chemistry of feedstock cell walls. Furthermore, improving both the catalytic potential of microbial communities that populate biodigester reactors and the efficiency of pre-treatments used in bioethanol production may improve bioconversion rates and yields. Toward this end, knowledge and characterization of carbohydrate-active enzymes (CAZymes) involved in dynamic biomass deconstruction is pivotal. Here we overview the use of common “-omics”-based methods for the study of lignocellulose-metabolizing communities and microorganisms, as well as methods for annotation and discovery of CAZymes, and accurate prediction of CAZyme function. Emerging approaches for analysis of large datasets, including metagenome-assembled genomes, are also discussed. Using complementary glycomic and meta-omic methods to characterize agricultural residues and the microbial communities that digest them provides promising streams of research to maximize value and energy extraction from crop waste streams.

Isolation and Characterization of Plant Cell Walls and Cell Wall Components

1988 ◽  
pp. 3-40 ◽  
Author(s):  
WILLIAM S. YORK ◽  
ALAN G. DARVILL ◽  
MICHAEL MCNEIL ◽  
THOMAS T. STEVENSON ◽  
PETER ALBERSHEIM
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Cell Walls ◽  
Plant Cell Walls ◽  
Cell Wall Components ◽  
Isolation And Characterization ◽  
Wall Components

Isolation and characterization of plant cell walls and cell wall components

1986 ◽  
pp. 3-40 ◽  
Author(s):  
William S. York ◽  
Alan G. Darvill ◽  
Michael McNeil ◽  
Thomas T. Stevenson ◽  
Peter Albersheim
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Cell Walls ◽  
Plant Cell Walls ◽  
Cell Wall Components ◽  
Isolation And Characterization ◽  
Wall Components

scholarly journals The endogenous galactofuranosidase GlfH1 hydrolyzes mycobacterial arabinogalactan

2020 ◽  
Vol 295 (15) ◽  
pp. 5110-5123 ◽  
Author(s):  
Lin Shen ◽  
Albertus Viljoen ◽  
Sydney Villaume ◽  
Maju Joe ◽  
Iman Halloum ◽  
...  
Keyword(s):  
Cell Wall ◽  
Structural Changes ◽  
Cell Envelope ◽  
Wall Structure ◽  
Tubercle Bacillus ◽  
Bioinformatics Analyses ◽  
The Past ◽  
Biochemical Assays ◽  
Mycobacterial Protein

Despite impressive progress made over the past 20 years in our understanding of mycolylarabinogalactan-peptidoglycan (mAGP) biogenesis, the mechanisms by which the tubercle bacillus Mycobacterium tuberculosis adapts its cell wall structure and composition to various environmental conditions, especially during infection, remain poorly understood. Being the central portion of the mAGP complex, arabinogalactan (AG) is believed to be the constituent of the mycobacterial cell envelope that undergoes the least structural changes, but no reports exist supporting this assumption. Herein, using recombinantly expressed mycobacterial protein, bioinformatics analyses, and kinetic and biochemical assays, we demonstrate that the AG can be remodeled by a mycobacterial endogenous enzyme. In particular, we found that the mycobacterial GlfH1 (Rv3096) protein exhibits exo-β-d-galactofuranose hydrolase activity and is capable of hydrolyzing the galactan chain of AG by recurrent cleavage of the terminal β-(1,5) and β-(1,6)-Galf linkages. The characterization of this galactosidase represents a first step toward understanding the remodeling of mycobacterial AG.

scholarly journals Novel tool to quantify cell wall porosity relates wall structure to cell growth and drug uptake

2019 ◽  
Vol 218 (4) ◽  
pp. 1408-1421 ◽  
Author(s):  
Xiaohui Liu ◽  
Jiazhou Li ◽  
Heyu Zhao ◽  
Boyang Liu ◽  
Thomas Günther-Pomorski ◽  
...  
Keyword(s):  
Cell Wall ◽  
Cell Walls ◽  
Dynamic Structure ◽  
Cell Types ◽  
Antifungal Drugs ◽  
Drug Uptake ◽  
Wall Structure ◽  
Quenching Efficiency ◽  
Model Plant Arabidopsis Thaliana ◽  
Cell Wall Porosity

Even though cell walls have essential functions for bacteria, fungi, and plants, tools to investigate their dynamic structure in living cells have been missing. Here, it is shown that changes in the intensity of the plasma membrane dye FM4-64 in response to extracellular quenchers depend on the nano-scale porosity of cell walls. The correlation of quenching efficiency and cell wall porosity is supported by tests on various cell types, application of differently sized quenchers, and comparison of results with confocal, electron, and atomic force microscopy images. The quenching assay was used to investigate how changes in cell wall porosity affect the capability for extension growth in the model plant Arabidopsis thaliana. Results suggest that increased porosity is not a precondition but a result of cell extension, thereby providing new insight on the mechanism plant organ growth. Furthermore, it was shown that higher cell wall porosity can facilitate the action of antifungal drugs in Saccharomyces cerevisiae, presumably by facilitating uptake.

scholarly journals Investigation of the Mechanical Properties of Flax Cell Walls during Plant Development: The Relation between Performance and Cell Wall Structure

Fibers ◽  
2018 ◽  
Vol 6 (1) ◽  
pp. 6 ◽  
Author(s):  
Camille Goudenhooft ◽  
David Siniscalco ◽  
Olivier Arnould ◽  
Alain Bourmaud ◽  
Olivier Sire ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Cell Wall ◽  
Plant Development ◽  
Cell Walls ◽  
Cell Wall Structure ◽  
Wall Structure

scholarly journals Characterization of Monolaurin Resistance in Enterococcus faecalis

2007 ◽  
Vol 73 (17) ◽  
pp. 5507-5515 ◽  
Author(s):  
Muriel Dufour ◽  
Janet M. Manson ◽  
Philip J. Bremer ◽  
Jean-Pierre Dufour ◽  
Gregory M. Cook ◽  
...  
Keyword(s):  
Cell Wall ◽  
Cell Surface ◽  
Enterococcus Faecalis ◽  
Cell Surface Hydrophobicity ◽  
Surface Hydrophobicity ◽  
Wall Structure ◽  
Transmission Electron ◽  
Serious Infections ◽  
Autolytic Activity

ABSTRACT There is increasing concern regarding the presence of vancomycin-resistant enterococci in domestically farmed animals, which may act as reservoirs and vehicles of transmission for drug-resistant enterococci to humans, resulting in serious infections. In order to assess the potential for the use of monolaurin as a food preservative, it is important to understand both its target and potential mechanisms of resistance. A Tn917 mutant library of Enterococcus faecalis AR01/DGVS was screened for resistance (MIC, >100 μg/ml) to monolaurin. Three mutants were identified as resistant to monolaurin and were designated DGRM2, DGRM5, and DGRM12. The gene interrupted in all three mutants was identified as traB, which encodes an E. faecalis pheromone shutdown protein and whose complementation in trans restored monolaurin sensitivity in all three mutants. DGRM2 was selected for further characterization. E. faecalis DGRM2 showed increased resistance to gentamicin and chloramphenicol (inhibitors of protein synthesis), while no difference in the MIC was observed with the cell wall-active antibiotics penicillin and vancomycin. E. faecalis AR01/DGVS and DGRM2 were shown to have similar rates (30% cell lysis after 4 h) of cell autolytic activity when activated by monolaurin. Differences in cell surface hydrophobicity were observed between the wild type and the mutant, with the cell surface of the parent strain being significantly more hydrophobic. Analysis of the cell wall structure of DGRM2 by transmission electron microscopy revealed an increase in the apparent cell wall thickness and contraction of its cytoplasm. Taken together, these results suggest that the increased resistance of DGRM2 was due to a change in cell surface hydrophobicity, consequently limiting the diffusion of monolaurin to a potential target in the cytoplasmic membrane and/or cytoplasm of E. faecalis.

Die gemeinsame Wurzel der Lyse von Escherichia coli durch Penicillin oder durch Phagen

1957 ◽  
Vol 12 (7) ◽  
pp. 421-427 ◽  
Author(s):  
W. Weidel ◽  
J. Primosigh
Keyword(s):  
Cell Wall ◽  
Cell Walls ◽  
Building Blocks ◽  
Diaminopimelic Acid ◽  
Wall Structure ◽  
Gram Positive ◽  
E Coli ◽  
Growing Cell ◽  
Cell Wall Disruption ◽  
Entire Cell

One of the two layers of the E. coli B cell wall is shown to possess the chemical composition typical of a gram-positive microorganism. It is this layer which lends support and strength to the entire cell wall structure, its rigidity depending up on the incorporation of building blocks made up from alanine, glutamic acid, diaminopimelic acid, muramic acid and glucosamine.Phage enzyme is an agent capable of removing these stabilizing units from the „gram-positive “ layer, thereby causing it to collapse. Penicillin appears to prevent the biosynthetic incorporation of the same stabilizing units into growing cell walls, thus producing eventually the effect of cell wall disruption in a basically similar way.The rather manifold aspects of these findings are discussed at some length.

scholarly journals Chilling Injury in Peaches: A Cytochemical and Ultrastructural Cell Wall Study

1992 ◽  
Vol 117 (1) ◽  
pp. 114-118 ◽  
Author(s):  
J.G. Luza ◽  
R. van Gorsel ◽  
V.S. Polito ◽  
A.A. Kader
Keyword(s):  
Cell Wall ◽  
Cell Walls ◽  
Prunus Persica ◽  
Periodic Acid ◽  
Chilling Injury ◽  
Middle Lamella ◽  
Wall Structure ◽  
Positive Staining ◽  
Intercellular Matrix ◽  
Parenchyma Cells

Fruits of mid- (`O'Henry'), late (`Airtime'), and extra-late-season (`Autumn Gem') peach [Prunus persica (L.) Batsch] cultivars were examined for changes in cell wall structure and cytochemistry that accompany the onset of mealiness and leatheriness of the mesocarp due to chilling injury. The peaches were stored at 10C for up to 18 days or at SC for up to 29 days. Plastic-embedded sections were stained by the Schiff's-periodic acid reaction, Calcofluor white MR2, and Coriphosphine to demonstrate total insoluble carbohydrates, ß-1,4 glucans, and pectins, respectively. Mealiness was characterized by separation of mesocarp parenchyma cells leading to increased intercellular spaces and accumulation of pectic substances in the intercellular matrix. Little structural change was apparent in the cellulosic component of the cell walls of these fruits. In leathery peaches, the mesocarp parenchyma cells collapsed, intercellular space continued to increase, and pectin-positive staining in the intercellular matrix increased greatly. In addition, the component of the cell walls that stained positively for ß-1,4 glucans became thickened relative to freshly harvested or mealy fruit. At the ultrastructural level, dissolution of the middle lamella, cell separation, irregular thickening of the primary wall, and plasmolysis of the mesocarp parenchyma cells were seen as internal breakdown progressed.

scholarly journals Aplikasi Kalsium dan NAA untuk Mengendalikan Getah Kuning Buah Manggis (Garcinia mangostana L.)

2018 ◽  
Vol 9 (1) ◽  
pp. 10-18
Author(s):  
Yulinda Tanari ◽  
Darda Efendi ◽  
Roedhy Poerwanto ◽  
Didy Sopandie ◽  
Ketty Suketi
Keyword(s):  
Cell Wall ◽  
Cell Division ◽  
Cell Walls ◽  
Block Design ◽  
Wall Structure ◽  
Sink Strength ◽  
Naphthaleneacetic Acid ◽  
Garcinia Mangostana ◽  
Random Block ◽  
Random Block Design

ABSTRACTThe yellow sap is produced naturally in mangosteen organ except in the root. The yellow sap contaminated the aryl and rind if the epithelial cell walls rupture due to deficiency of calcium (Ca). Calcium is one of structural component of cell walls, whereas naphthaleneacetic acid (NAA) has its role in improving cell division and cell elongation. Interaction of Ca and NAA can improve sink strength and capacity because the newly formed cells need Ca to construct wall structure. This experiment aimed at finding out the effect of Ca and NAA applications in reducing the contamination of yellow sap in mangosteen. The experiment was conducted by using factorial random block design consisting of 2 factors and 3 replications. The first factor was Ca dosage (0 and 4.8 kg/tree), and the second factor was NAA concentration (0, 200, 400 and 600 ppm). The results showed that application of 4.8 Ca/tree and 200 ppm NAA as much as 5 ml / fruit effectively improve the content of Ca pectate in pericarp, reduced the percentage of yellow sap contamination on the fruit segment, aryl and rind to 0% and 12.3% respectively compared to control (17.8% on fruit segment, 36.8% on aryl and 56.1% on rind).Key words: aryl, Ca pectate, cell wall, middle lamela.ABSTRAKGetah kuning adalah getah yang dihasilkan secara alami pada setiap organ manggis, kecuali pada akar. Getah kuning akan keluar dan mencemari aril serta kulit jika dinding sel epitel pecah karena kekurangan kalsium (Ca). Kalsium adalah komponen dinding sel, berperan dalam struktur dan permeabilitas membran sedangkan asam naftalenasetat (NAA) berperan penting dalam meningkatkan pembelahan dan pembesaran sel. Interaksi keduanya dapat meningkatkan kapasitas sink buah karena sel yang baru terbentuk membutuhkan Ca dalam menyusun struktur dinding sel. Percobaan bertujuan untuk mengetahui pengaruh aplikasi Ca dan NAA dalam menurunkan cemaran getah kuning manggis. Percobaan menggunakan rancangan acak kelompok faktorial 2 faktor dengan 3 ulangan. Faktor ke-1 yaitu dosis Ca (0 dan 4.8 kg Ca/pohon) dan faktor ke-2 yaitu konsentrasi NAA (0, 200, 400 dan 600 ppm) dengan volume semprot 5 ml perbuah. Hasil percobaan menunjukkan bahwa aplikasi 4.8 kg Ca/pohon dengan NAA 200 ppm sebanyak 5 ml/buah efektif meningkatkan kandungan Ca pektat perikarp dan menurunkan persentase buah tercemar getah kuning menjadi 0% pada juring dan aril serta 12.3% pada kulit dibandingkan dengan perlakuan kontrol (17.8% pada juring, 36.8% pada aril dan 56.1% pada kulit buah).Kata kunci: aril, Ca pektat, dinding sel, lamela tengah

scholarly journals Staphylococcus aureus cell wall structure and dynamics during host-pathogen interaction

2021 ◽  
Vol 17 (3) ◽  
pp. e1009468
Author(s):  
Joshua A. F. Sutton ◽  
Oliver T. Carnell ◽  
Lucia Lafage ◽  
Joe Gray ◽  
Jacob Biboy ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Cell Wall ◽  
Cell Walls ◽  
Ex Vivo ◽  
Cell Wall Structure ◽  
Wall Structure ◽  
Bacterial Cells ◽  
Human Macrophages ◽  
Structure And Dynamics

Peptidoglycan is the major structural component of the Staphylococcus aureus cell wall, in which it maintains cellular integrity, is the interface with the host, and its synthesis is targeted by some of the most crucial antibiotics developed. Despite this importance, and the wealth of data from in vitro studies, we do not understand the structure and dynamics of peptidoglycan during infection. In this study we have developed methods to harvest bacteria from an active infection in order to purify cell walls for biochemical analysis ex vivo. Isolated ex vivo bacterial cells are smaller than those actively growing in vitro, with thickened cell walls and reduced peptidoglycan crosslinking, similar to that of stationary phase cells. These features suggested a role for specific peptidoglycan homeostatic mechanisms in disease. As S. aureus penicillin binding protein 4 (PBP4) has reduced peptidoglycan crosslinking in vitro its role during infection was established. Loss of PBP4 resulted in an increased recovery of S. aureus from the livers of infected mice, which correlated with enhanced fitness within murine and human macrophages. Thicker cell walls correlate with reduced activity of peptidoglycan hydrolases. S. aureus has a family of 4 putative glucosaminidases, that are collectively crucial for growth. Loss of the major enzyme SagB, led to attenuation during murine infection and reduced survival in human macrophages. However, loss of the other three enzymes Atl, SagA and ScaH resulted in clustering dependent attenuation, in a zebrafish embryo, but not a murine, model of infection. A combination of pbp4 and sagB deficiencies resulted in a restoration of parental virulence. Our results, demonstrate the importance of appropriate cell wall structure and dynamics during pathogenesis, providing new insight to the mechanisms of disease.

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