scholarly journals Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

2020 ◽  
Author(s):  
Live H. Hagen ◽  
Charles G. Brooke ◽  
Claire Shaw ◽  
Angela D. Norbeck ◽  
Hailan Piao ◽  
...  
Keyword(s):  
Plant Cell Wall ◽  
Plant Biomass ◽  
Soluble Sugars ◽  
Rumen Bacteria ◽  
Anaerobic Fungi ◽  
Host Animal ◽  
Bacterial Populations ◽  
Domain Specific ◽  
Gene Catalogue ◽  
Ruminal Degradation

AbstractThe rumen harbors a complex microbial mixture of archaea, bacteria, protozoa and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 hours in nylon bags within the rumen of cannulated dairy cows. Across a gene catalogue covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of polysaccharides such as hemicellulose, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8 and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggests that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

scholarly journals Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

2020 ◽  
Author(s):  
Live H. Hagen ◽  
Charles G. Brooke ◽  
Claire A. Shaw ◽  
Angela D. Norbeck ◽  
Hailan Piao ◽  
...  
Keyword(s):  
Plant Cell Wall ◽  
Plant Biomass ◽  
Soluble Sugars ◽  
Rumen Bacteria ◽  
Anaerobic Fungi ◽  
Host Animal ◽  
Bacterial Populations ◽  
Domain Specific ◽  
Gene Catalog ◽  
Ruminal Degradation

Abstract The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

scholarly journals Toward combined delignification and saccharification of wheat straw by a laccase-containing designer cellulosome

2016 ◽  
Vol 113 (39) ◽  
pp. 10854-10859 ◽  
Author(s):  
Lital Davidi ◽  
Sarah Moraïs ◽  
Lior Artzi ◽  
Doriv Knop ◽  
Yitzhak Hadar ◽  
...  
Keyword(s):  
Wheat Straw ◽  
Alternative Fuels ◽  
Plant Cell Wall ◽  
Plant Biomass ◽  
Soluble Sugars ◽  
Spatial Proximity ◽  
Aerobic Bacterium ◽  
Lignocellulose Conversion ◽  
Wide Range ◽  
Designer Cellulosome

Efficient breakdown of lignocellulose polymers into simple molecules is a key technological bottleneck limiting the production of plant-derived biofuels and chemicals. In nature, plant biomass degradation is achieved by the action of a wide range of microbial enzymes. In aerobic microorganisms, these enzymes are secreted as discrete elements in contrast to certain anaerobic bacteria, where they are assembled into large multienzyme complexes termed cellulosomes. These complexes allow for very efficient hydrolysis of cellulose and hemicellulose due to the spatial proximity of synergistically acting enzymes and to the limited diffusion of the enzymes and their products. Recently, designer cellulosomes have been developed to incorporate foreign enzymatic activities in cellulosomes so as to enhance lignocellulose hydrolysis further. In this study, we complemented a cellulosome active on cellulose and hemicellulose by addition of an enzyme active on lignin. To do so, we designed a dockerin-fused variant of a recently characterized laccase from the aerobic bacteriumThermobifida fusca. The resultant chimera exhibited activity levels similar to the wild-type enzyme and properly integrated into the designer cellulosome. The resulting complex yielded a twofold increase in the amount of reducing sugars released from wheat straw compared with the same system lacking the laccase. The unorthodox use of aerobic enzymes in designer cellulosome machinery effects simultaneous degradation of the three major components of the plant cell wall (cellulose, hemicellulose, and lignin), paving the way for more efficient lignocellulose conversion into soluble sugars en route to alternative fuels production.

scholarly journals Colocalization and Disposition of Cellulosomes in Clostridium clariflavum as Revealed by Correlative Superresolution Imaging

mBio ◽  
2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Lior Artzi ◽  
Tali Dadosh ◽  
Elad Milrot ◽  
Sarah Moraïs ◽  
Smadar Levin-Zaidman ◽  
...  
Keyword(s):  
Cell Surface ◽  
Bacterial Cell ◽  
Plant Cell Wall ◽  
Plant Biomass ◽  
Soluble Sugars ◽  
Attractive Alternative ◽  
Cellulolytic Bacteria ◽  
Extracellular Medium ◽  
Bacterial Cell Surface ◽  
Clostridium Clariflavum

ABSTRACTCellulosomes are multienzyme complexes produced by anaerobic, cellulolytic bacteria for highly efficient breakdown of plant cell wall polysaccharides.Clostridium clariflavumis an anaerobic, thermophilic bacterium that produces the largest assembled cellulosome complex in nature to date, comprising three types of scaffoldins: a primary scaffoldin, ScaA; an adaptor scaffoldin, ScaB; and a cell surface anchoring scaffoldin, ScaC. This complex can contain 160 polysaccharide-degrading enzymes. In previous studies, we proposed potential types of cellulosome assemblies inC. clariflavumand demonstrated that these complexes are released into the extracellular medium. In the present study, we explored the disposition of the highly structured, four-tiered cell-anchored cellulosome complex of this bacterium. Four separate, integral cellulosome components were subjected to immunolabeling: ScaA, ScaB, ScaC, and the cellulosome’s most prominent enzyme, GH48. Imaging of the cells by correlating scanning electron microscopy and three-dimensional (3D) superresolution fluorescence microscopy revealed that some of the protuberance-like structures on the cell surface represent cellulosomes and that the components are highly colocalized and organized by a defined hierarchy on the cell surface. The display of the cellulosome on the cell surface was found to differ between cells grown on soluble or insoluble substrates. Cell growth on microcrystalline cellulose and wheat straw exhibited dramatic enhancement in the amount of cellulosomes displayed on the bacterial cell surface.IMPORTANCEConversion of plant biomass into soluble sugars is of high interest for production of fermentable industrial materials, such as biofuels. Biofuels are a very attractive alternative to fossil fuels, both for recycling of agricultural wastes and as a source of sustainable energy. Cellulosomes are among the most efficient enzymatic degraders of biomass known to date, due to the incorporation of a multiplicity of enzymes into a potent, multifunctional nanomachine. The intimate association with the bacterial cell surface is inherent in its efficient action on lignocellulosic substrates, although this property has not been properly addressed experimentally. The dramatic increase in cellulosome performance on recalcitrant feedstocks is critical for the design of cost-effective processes for efficient biomass degradation.

Biochemical Composition and Phosphorus Use Efficiency in Some Mixtures

2016 ◽  
Vol 5 (07) ◽  
pp. 4694 ◽  
Author(s):  
Viliana Vasileva ◽  
Anna Ilieva
Keyword(s):  
Perennial Ryegrass ◽  
Biochemical Composition ◽  
Plant Biomass ◽  
Soluble Sugars ◽  
Subterranean Clover ◽  
Water Soluble ◽  
Birdsfoot Trefoil ◽  
Phosphorus Use Efficiency ◽  
Forage Crops ◽  
Use Efficiency

In pot trial the biochemical composition and phosphorus use efficiency of birdsfoot trefoil, sainfoin and subterranean clover grown pure and in mixtures with perennial ryegrass in the next ratios were studied in the Institute of Forage Crops, Pleven, Bulgaria: birdsfoot trefoil + perennial ryegrass (50:50%); sainfoin + perennial ryegrass (50:50%); subterranean clover + perennial ryegrass (50:50%); birdsfoot trefoil + subterranean clover + perennial ryegrass (33:33:33%); sainfoin + subterranean clover + perennial ryegrass (33:33:33%). The highest crude protein content was found in the aboveground mass of birdsfoot trefoil (19.17%) and sainfoin (19.30%). The water soluble sugars contents in mixtures was found higher compared to the pure grown legumes. Birdsfoot trefoil showed the highest phosphorus use efficiency for plant biomass accumulation and nodules formation. In mixtures the phosphorus use efficiency was found be higher as compared to the same in pure grown legumes.

scholarly journals Some factors influencing the chemical composition of mixed rumen bacteria

1974 ◽  
Vol 31 (1) ◽  
pp. 27-34 ◽  
Author(s):  
R. H. Smith ◽  
A. B. Mcallan
Keyword(s):  
Chemical Composition ◽  
Dry Matter ◽  
Rumen Bacteria ◽  
Host Animal ◽  
Adult Cattle ◽  
Total N ◽  
Adult Sheep ◽  
Factors Influencing ◽  
Mixed Bacteria ◽  
Ciliate Protozoa

1. Sheep, cows and calves fitted with rumen cannulas were given diets mostly containing 10–16 g nitrogen/kg dry matter and consisting of roughage and cereals. Mixed bacteria were separated from samples of their rumen contents.2. Bacteria taken 4–6 h after a feed from calves which were kept in an experimental calf-house with no contact with adult animals (environment A) contained more α-dextran, less total N and higher nucleic acid:total N ratios than similar bacteria from calves reared in contact with adult sheep (environment C) but otherwise treated in an identical way.3. Mixed bacteria taken 4–6 h after a feed from sheep and cows were similar in composition, with respect to nitrogenous components, to those from the ‘environment C’ calves. This composition did not vary significantly when diets containing differing proportions of roughage were given.4. The ‘environment A’ calves were free of ciliate protozoa. When they were placed in contact with, and were inoculated with rumen contents from, adult cattle (environment B), they rapidly developed a normal protozoal population and the chemical composition of their rumen bacteria became like that of the bacteria from the ‘environment C’ calves.5. Mixed bacteria taken just before a feed, from either cows or ‘environment A’ calves, showed significantly lower RNA-N:total N ratios and slightly (but not usually significantly) higher DNA-N:total N ratios than bacteria taken 4–6 h after feeding. Total N contents of the bacteria did not change consistently with time after feeding.6. The possible significance of these differences in relation to the nutrition of the host animal is discussed.

scholarly journals Effects of static magnetic field on growth, some biochemical and antioxidant system in lemon balm (Melissa officinalis L.) seedlings

2021 ◽  
Vol 20 (1) ◽  
pp. 71-80
Author(s):  
Anousheh Zakeri ◽  
Ramazan-Ali Khavari-Nejad ◽  
Sara Saadatmand ◽  
Fatemeh Nouri Kootanaee ◽  
Rouzbeh Abbaszadeh
Keyword(s):  
Magnetic Field ◽  
Phenolic Compounds ◽  
Static Magnetic Field ◽  
Plant Biomass ◽  
Soluble Sugar ◽  
Soluble Sugars ◽  
Antioxidant Defense System ◽  
Total Soluble Sugars ◽  
Lemon Balm ◽  
Total Soluble Sugar

The effects of magnetic waves as natural environmental factors on the Earths are not well known on plant growth and development. The present study was carried out to evaluate the effects of static magnetic field (SMF) treatment (4 and 6 mT for 30 and 120 min per day) for eight days on the biomass production, proline contents and total soluble sugar, phenolic compounds, accumulation of H2O2 and MDA along with activity of antioxidant enzymes in lemon balm seedlings. Our results showed that SMF treatments, especially 6 mT and 120 min duration, increased the plant biomass, proline contents, phenolic compounds, H2O2 and MDA accumulation, and reduced the contents of total soluble sugars. The SMF application also increased the activity of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR) enzymes compared to untreated seedlings. Our results suggest that SMF treatments induces the antioxidant defense system in the lemon balm seedlings and, by changing the plant metabolism, improves the early vigor of seedlings.

Feruloyl and p-coumaroyl esterase from anaerobic fungi in relation to plant cell wall degradation

1990 ◽  
Vol 33 (3) ◽  
pp. 345-351 ◽  
Author(s):  
William S. Borneman ◽  
Roy D. Hartley ◽  
W. Herbert Morrison ◽  
Danny E. Akin ◽  
Lars G. Ljungdahl
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Anaerobic Fungi ◽  
Cell Wall Degradation ◽  
Plant Cell Wall Degradation

Identification of copper-containing oxidoreductases in the secretomes of three Colletotrichum species with a focus on copper radical oxidases for the biocatalytic production of fatty aldehydes

2021 ◽  
Author(s):  
David Ribeaucourt ◽  
Safwan Saker ◽  
David Navarro ◽  
Bastien Bissaro ◽  
Elodie Drula ◽  
...  
Keyword(s):  
Time Course ◽  
Plant Cell Wall ◽  
Plant Biomass ◽  
Recombinant Expression ◽  
Primary Objective ◽  
Primary Alcohols ◽  
Fungal Strains ◽  
Fatty Aldehydes ◽  
Initial Objective ◽  
Biocatalytic Production

Copper Radical Alcohol Oxidases (CRO-AlcOx), which have been recently discovered among fungal phytopathogens are attractive for the production of fragrant fatty aldehydes. With the initial objective to investigate the secretion of CRO-AlcOx by natural fungal strains, we undertook time-course analyses of the secretomes of three Colletotrichum species ( C. graminicola , C. tabacum and C. destructivum) using proteomics. The addition of a copper-manganese-ethanol mixture in absence of any plant-biomass mimicking compounds to Colletotrichum cultures unexpectedly induced the secretion of up to 400 proteins, 29-52% of which were carbohydrate-active enzymes (CAZymes), including a wide diversity of copper-containing oxidoreductases from the auxiliary activities (AA) class (AA1, AA3, AA5, AA7, AA9, AA11-AA13, AA16). Under these specific conditions, while a CRO-glyoxal oxidase from the AA5_1 subfamily was among the most abundantly secreted proteins, the targeted AA5_2 CRO-AlcOx were secreted at lower levels, suggesting heterologous expression as a more promising strategy for CRO-AlcOx production and utilization. C. tabacum and C. destructivum CRO-AlcOx were thus expressed in Pichia pastoris and their preference toward both aromatic and aliphatic primary alcohols was assessed. The CRO-AlcOx from C. destructivum was further investigated in applied settings, revealing a full conversion of C6 and C8 alcohols into their corresponding fragrant aldehydes. IMPORTANCE In the context of the industrial shift toward greener processes, the biocatalytic production of aldehydes is of utmost interest owing to their importance for their use as flavors and fragrances ingredients. CRO-AlcOx have the potential to become platform enzymes for the oxidation of alcohols to aldehydes. However, the secretion of CRO-AlcOx by natural fungal strains has never been explored, while the use of crude fungal secretomes is an appealing approach for industrial application to alleviate various costs pertaining to biocatalysts production. While investigating this primary objective, the secretomics studies revealed unexpected results showing that under the oxidative-stressful conditions we probed, Colletotrichum species can secrete a broad diversity of copper-containing enzymes (laccases, sugar oxidoreductases, LPMOs) usually assigned to “plant-cell wall degradation”, despite the absence of any plant-biomass mimicking compound, and only little amount of CRO-AlcOx were secreted, pointing out at recombinant expression as the most promising path for their biocatalytic application.

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.

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