scholarly journals Functional Diversity of Carbohydrate-Active Enzymes Enabling a Bacterium to Ferment Plant Biomass

PLoS Genetics ◽  
2014 ◽  
Vol 10 (11) ◽  
pp. e1004773 ◽  
Author(s):  
Magali Boutard ◽  
Tristan Cerisy ◽  
Pierre-Yves Nogue ◽  
Adriana Alberti ◽  
Jean Weissenbach ◽  
...  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maria Lorenza Leal Motta ◽  
Jaire Alves Ferreira Filho ◽  
Ricardo Rodrigues de Melo ◽  
Leticia Maria Zanphorlin ◽  
Clelton Aparecido dos Santos ◽  
...  

AbstractTrichoderma genus fungi present great potential for the production of carbohydrate-active enzymes (CAZYmes), including glycoside hydrolase (GH) family members. From a renewability perspective, CAZYmes can be biotechnologically exploited to convert plant biomass into free sugars for the production of advanced biofuels and other high-value chemicals. GH54 is an attractive enzyme family for biotechnological applications because many GH54 enzymes are bifunctional. Thus, GH54 enzymes are interesting targets in the search for new enzymes for use in industrial processes such as plant biomass conversion. Herein, a novel metal-dependent GH54 arabinofuranosidase (ThABF) from the cellulolytic fungus Trichoderma harzianum was identified and biochemically characterized. Initial in silico searches were performed to identify the GH54 sequence. Next, the gene was cloned and heterologously overexpressed in Escherichia coli. The recombinant protein was purified, and the enzyme’s biochemical and biophysical properties were assessed. GH54 members show wide functional diversity and specifically remove plant cell substitutions including arabinose and galactose in the presence of a metallic cofactor. Plant cell wall substitution has a major impact on lignocellulosic substrate conversion into high-value chemicals. These results expand the known functional diversity of the GH54 family, showing the potential of a novel arabinofuranosidase for plant biomass degradation.


2021 ◽  
Vol 9 ◽  
Author(s):  
Edimar A. Moreira ◽  
Gabriela F. Persinoti ◽  
Letícia R. Menezes ◽  
Douglas A. A. Paixão ◽  
Thabata M. Alvarez ◽  
...  

Lignocellulose digestion in termites is achieved through the functional synergy between gut symbionts and host enzymes. However, some species have evolved additional associations with nest microorganisms that collaborate in the decomposition of plant biomass. In a previous study, we determined that plant material packed with feces inside the nests of Cornitermes cumulans (Syntermitinae) harbors a distinct microbial assemblage. These food nodules also showed a high hemicellulolytic activity, possibly acting as an external place for complementary lignocellulose digestion. In this study, we used a combination of ITS sequence analysis, metagenomics, and metatranscriptomics to investigate the presence and differential expression of genes coding for carbohydrate-active enzymes (CAZy) in the food nodules and the gut of workers and soldiers. Our results confirm that food nodules express a distinct set of CAZy genes suggesting that stored plant material is initially decomposed by enzymes that target the lignin and complex polysaccharides from fungi and bacteria before the passage through the gut, where it is further targeted by a complementary set of cellulases, xylanases, and esterases produced by the gut microbiota and the termite host. We also showed that the expression of CAZy transcripts associated to endoglucanases and xylanases was higher in the gut of termites than in the food nodules. An additional finding in this study was the presence of fungi in the termite gut that expressed CAZy genes. This study highlights the importance of externalization of digestion by nest microbes and provides new evidence of complementary digestion in the context of higher termite evolution.


Author(s):  
Camila L. Corrêa ◽  
Glaucia E. O. Midorikawa ◽  
Edivaldo Ximenes Ferreira Filho ◽  
Eliane Ferreira Noronha ◽  
Gabriel S. C. Alves ◽  
...  

2014 ◽  
Vol 1 (1) ◽  
pp. 907-945
Author(s):  
M.-A. de Graaff ◽  
J. Adkins ◽  
P. Kardol ◽  
H. L. Throop

Abstract. Loss of biodiversity can impact ecosystem functioning, such as altering carbon (C) cycling rates. Soils are the largest terrestrial C reservoir, containing more C globally than the biotic and atmospheric pools together. As such, soil C cycling, and the processes controlling it, have the potential to affect atmospheric CO2 concentrations and subsequent climate change. Despite the growing evidence of links between plant diversity and soil C cycling, there is a dearth of information on whether similar relationships exist between biodiversity of soil organisms (microbes and soil fauna) and C cycling. This is despite increasing recognition that soil communities display high levels of both taxonomic and functional diversity and are key drivers of fluxes of C between the atmosphere and terrestrial ecosystems. Here, we used meta-analysis and regression analysis to quantitatively assess how soil biodiversity affects soil C cycling pools and processes (i.e., soil C respiration, litter decomposition, and plant biomass). We compared the response of pool amd process variables to changes in biodiversity both within and across trophic groups of organisms. Overall, loss of soil diversity significantly reduced soil C respiration (−27.5%) and plant tissue decomposition (−18%), but did not affect above- and belowground plant biomass. Detailed analyses showed that loss of within-group biodiversity significantly reduced soil C respiration, while loss of across-group diversity did not. Decomposition was negatively affected by losses of both within-group and across-group diversity. Further, loss of microbial diversity strongly reduced soil C respiration (−41%). In contrast, plant tissue decomposition was negatively affected by loss of soil faunal diversity, but was unaffected by loss of microbial diversity. Taken together, our findings show that loss of soil biodiversity can strongly affect soil C cycling processes, and highlight the importance of diversity across organismal groups for maintaining full C cycling functionality. However, our understanding of the complex relationships between soil biodiversity and C cycling processes is currently limited by the sheer number of methodological concerns associated with these studies, which can greatly overestimate or underestimate the impact of soil biodiversity on soil C cycling. These limitations present challenges to extrapolation to natural field settings. Future studies should attempt to further elucidate the relative importance of taxonomic diversity vs. functional diversity.


2020 ◽  
Author(s):  
Maria Lorenza Leal Motta ◽  
Jaire Alves Ferreira Filho ◽  
Ricardo Rodrigues de Melo ◽  
Leticia Maria Zanphorlin Murakami ◽  
Clelton Aparecido dos Santos ◽  
...  

AbstractTrichoderma genus fungi present great potential for the production of carbohydrate-active enzymes (CAZYmes), including glycoside hydrolase (GH) family members. From a renewability perspective, CAZYmes can be biotechnologically exploited to convert plant biomass into free sugars for the production of advanced biofuels and other high-value chemicals. GH54 is an attractive enzyme family for biotechnological applications because many GH54 enzymes are bifunctional. Thus, GH54 enzymes are interesting targets in the search for new enzymes for use in industrial processes such as plant biomass conversion. Herein, a novel metal-dependent GH54 arabinofuranosidase (ThABF) from the cellulolytic fungus Trichoderma harzianum was identified and biochemically characterized. Initial in silico searches were performed to identify the GH54 sequence. Next, the gene was cloned and heterologously overexpressed in Escherichia coli. The recombinant protein was purified, and the enzyme’s biochemical and biophysical properties were assessed. The GH54 members show wide functional diversity and specifically remove plant cell decorations including arabinose and galactose, in the presence of a metallic cofactor. Plant cell wall decoration have a major impact on lignocellulosic substrate conversion into high-value chemicals. These results expand the known functional diversity within the GH54 family, showing the potential of a novel arabinofuranosidase for plant biomass degradation.


Plants ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 53
Author(s):  
Leonardo H. Teixeira ◽  
Florencia A. Yannelli ◽  
Gislene Ganade ◽  
Johannes Kollmann

Ecosystem properties can be positively affected by plant functional diversity and compromised by invasive alien plants. We performed a community assembly study in mesocosms manipulating different functional diversity levels for native grassland plants (communities composed by 1, 2 or 3 functional groups) to test if functional dispersion could constrain the impacts of an invasive alien plant (Solidago gigantea) on soil fertility and plant community biomass via complementarity. Response variables were soil nutrients, soil water nutrients and aboveground biomass. We applied linear mixed-effects models to assess the effects of functional diversity and S. gigantea on plant biomass, soil and soil water nutrients. A structural equation model was used to evaluate if functional diversity and invasive plants affect soil fertility directly or indirectly via plant biomass and soil pH. Invaded communities had greater total biomass but less native plant biomass than uninvaded ones. While functional diversity increased nutrient availability in the soil solution of uninvaded communities, invasive plants reduced nutrient concentration in invaded soils. Functional diversity indirectly affected soil water but not soil nutrients via plant biomass, whereas the invader reduced native plant biomass and disrupted the effects of diversity on nutrients. Moreover, invasive plants reduced soil pH and compromised phosphate uptake by plants, which can contribute to higher phosphate availability and its possible accumulation in invaded soils. We found little evidence for functional diversity to constrain invasion impacts on nutrients and plant biomass. Restoration of such systems should consider other plant community features than plant trait diversity to reduce establishment of invasive plants.


2020 ◽  
Vol 8 (3) ◽  
pp. 385 ◽  
Author(s):  
Sara E. Blumer-Schuette

Plant polysaccharides continue to serve as a promising feedstock for bioproduct fermentation. However, the recalcitrant nature of plant biomass requires certain key enzymes, including cellobiohydrolases, for efficient solubilization of polysaccharides. Thermostable carbohydrate-active enzymes are sought for their stability and tolerance to other process parameters. Plant biomass degrading microbes found in biotopes like geothermally heated water sources, compost piles, and thermophilic digesters are a common source of thermostable enzymes. While traditional thermophilic enzyme discovery first focused on microbe isolation followed by functional characterization, metagenomic sequences are negating the initial need for species isolation. Here, we summarize the current state of knowledge about the extremely thermophilic genus Caldicellulosiruptor, including genomic and metagenomic analyses in addition to recent breakthroughs in enzymology and genetic manipulation of the genus. Ten years after completing the first Caldicellulosiruptor genome sequence, the tools required for systems biology of this non-model environmental microorganism are in place.


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