Large-scale phenotyping of 1,000 fungal strains for the degradation of non-natural, industrial compounds

Navarro, David; Chaduli, Delphine; Taussac, Sabine; Lesage‐Meessen, Laurence; Grisel, Sacha; Haon, Mireille; Callac, Philippe; Courtecuisse, Régis; Decock, Cony; Dupont, Joëlle; Richard‐Forget, Florence; Fournier, Jacques; Guimberteau, Jacques; Lechat, Christian; Moreau, Pierre‐Arthur; Pinson‐Gadais, Laëtitia; Rivoire, Bernard; Sage, Lucile; Welti, Stéphane; Rosso, Marie‐Noëlle; Berrin, Jean-Guy; Bissaro, Bastien; Favel, Anne

doi:10.21203/rs.3.rs-289168/v1

Cited by 3 publications

(3 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The U. maydis strain 521, which was provided by the CIRM-CF collection (strain BRFM1093) (50) was grown in 100 mL of Yeast Extract (10 g.L -1 ) / BactoPeptone (20 g.L -1 ) / Dextrose (20 g.L -1 ) (YPD medium) for 48 h at 28 °C in 250 mL-baffled Erlenmeyer flask under orbital agitation (150 rpm). Cells were then harvested and washed once in H2O by centrifugation (1,500 g , 10 min), counted and stored at 10 7 cells/mL in 20% glycerol at −80 °C as a working cell bank for long term preservation.…”

Section: Methodsmentioning

confidence: 99%

The maize pathogen Ustilago maydis secretes glycoside hydrolases and carbohydrate oxidases directed towards components of the fungal cell wall

Bissaro

Berrin

Grisel

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

Filamentous fungi are keystone microorganisms in the regulation of many processes occurring on Earth, such as plant biomass decay, pathogenesis as well as symbiotic associations. In many of these processes, fungi secrete carbohydrate-active enzymes (CAZymes) to modify and/or degrade carbohydrates. Ten years ago, while evaluating the potential of a secretome from the maize pathogen Ustilago maydis to supplement lignocellulolytic cocktails, we noticed it contained many unknown or poorly characterized CAZymes. Here, and after re-annotation of this dataset and detailed phylogenetic analyses, we observed that several CAZymes (including glycoside hydrolases and carbohydrate oxidases) are predicted to act on the fungal cell wall (FCW), notably on β-1,3-glucans. We heterologously produced and biochemically characterized two new CAZymes, called UmGH16_1-A and UmAA3_2-A. We show that UmGH16_1-A displays β-1,3-glucanase activity, with a preference for β-1,3-glucans with short β-1,6 substitutions, and UmAA3_2-A is a dehydrogenase catalyzing the oxidation of β-1,3- and β-1,6-gluco-oligosaccharides into the corresponding aldonic acids. Working on model β-1,3-glucans, we show that the linear oligosaccharide products released by UmGH16_1-A are further oxidized by UmAA3_2-A, bringing to light a putative biocatalytic cascade. Interestingly, analysis of available transcriptomics data indicates that both UmGH16_1-A and UmAA3_2-A are co-expressed, only during early stages of U. maydis infection cycle. Altogether, our results suggest that both enzymes are connected and that additional accessory activities still need to be uncovered to fully understand the biocatalytic cascade at play and its physiological role.ImportanceFilamentous fungi play a central regulatory role on Earth, notably in the global carbon cycle. Regardless of their lifestyle, filamentous fungi need to remodel their own cell wall (mostly composed of polysaccharides) to grow and proliferate. To do so, they must secrete a large arsenal of enzymes, most notably carbohydrate-active enzymes (CAZymes). However, research on fungal CAZymes over past decades has mainly focused on finding efficient plant biomass conversion processes while CAZymes directed at the fungus itself have remained little explored. In the present study, using the maize pathogen Ustilago maydis as model, we set off to evaluate the prevalence of CAZymes directed towards the fungal cell wall during growth of the fungus on plant biomass and characterized two new CAZymes active on fungal cell wall components. Our results suggest the existence of a biocatalytic cascade that remains to be fully understood.

show abstract

Section: Methodsmentioning

confidence: 99%

The maize pathogen Ustilago maydis secretes glycoside hydrolases and carbohydrate oxidases directed towards components of the fungal cell wall

Bissaro

Berrin

Grisel

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Fungal cell wall extraction. The U. maydis strain 521, which was provided by the CIRM-CF collection (strain BRFM1093) (54) was grown in 100 mL of yeast extract (10 g.L 21 )/BactoPeptone (20 g.L 21 )/ Dextrose (20 g.L 21 ) (YPD medium) for 48 h at 28°C in 250 mL-baffled Erlenmeyer flask under orbital agitation (150 rpm). Cells were then harvested and washed once in H 2 O by centrifugation (1,500 g, 10 min), counted and stored at 10 7 cells/mL in 20% glycerol at 280°C as a working cell bank for long term preservation.…”

Section: U Maydis Cazymes Directed At the Fungal Cell Wallmentioning

confidence: 99%

The Maize Pathogen Ustilago maydis Secretes Glycoside Hydrolases and Carbohydrate Oxidases Directed toward Components of the Fungal Cell Wall

Reyre

Grisel

Haon

et al. 2022

Appl Environ Microbiol

View full text Add to dashboard Cite

show abstract

“…However, for many plastics, biological processes for polymer degradation remain to be demonstrated commercially. With this in mind, scientists have been exploring the potential of microorganisms to biodegrade plastics ( 11 , 12 ).…”

Section: Introductionmentioning

confidence: 99%

PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation

et al. 2022

View full text Add to dashboard Cite

The number of publications reporting putative plastic-degrading microbes and proteins is continuously increasing, necessitating the compilation of these data and the development of tools to facilitate their analysis. We developed the PlasticDB web application to address this need, which comprises a database of microorganisms and proteins reported to biodegrade plastics. Associated metadata, such as the techniques utilized to assess biodegradation, the environmental source of microbial isolate and presumed thermophilic traits are also reported. Proteins in the database are categorized according to the plastic type they are reported to degrade. Each protein structure has been predicted in silico and can be visualized or downloaded for further investigation. In addition to standard database functionalities, such as searching, filtering and retrieving database records, we implemented several analytical tools that accept inputs, including gene, genome, metagenome, transcriptomes, metatranscriptomes and taxa table data. Users can now analyze their datasets for the presence of putative plastic-degrading species and potential plastic-degrading proteins and pathways from those species. Database URL:http://plasticdb.org.

show abstract

Large-scale phenotyping of 1,000 fungal strains for the degradation of non-natural, industrial compounds

Cited by 3 publications

References 43 publications

The maize pathogen Ustilago maydis secretes glycoside hydrolases and carbohydrate oxidases directed towards components of the fungal cell wall

The maize pathogen Ustilago maydis secretes glycoside hydrolases and carbohydrate oxidases directed towards components of the fungal cell wall

The Maize Pathogen Ustilago maydis Secretes Glycoside Hydrolases and Carbohydrate Oxidases Directed toward Components of the Fungal Cell Wall

PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation

Contact Info

Product

Resources

About