Proteomic enzyme analysis of the marine fungus Paradendryphiella salina reveals alginate lyase as a minimal adaptation strategy for brown algae degradation

Bo Pilgaard,Marlene Vuillemin,Nanna Rhein-Knudsen,Florian-Alexander Herbst,Lene Lange,Casper Wilkens,Anne S. Meyer

doi:10.1038/s41598-019-48823-9

Bo Pilgaard, Marlene Vuillemin + Show 5 more

Open Access

https://doi.org/10.1038/s41598-019-48823-9

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Abstract

We set out to investigate the genetic adaptations of the marine fungus Paradendryphiella salina CBS112865 for degradation of brown macroalgae. We performed whole genome and transcriptome sequencing and shotgun proteomic analysis of the secretome of P. salina grown on three species of brown algae and under carbon limitation. Genome comparison with closely related terrestrial fungi revealed that P. salina had a similar but reduced CAZyme profile relative to the terrestrial fungi except for the presence of three putative alginate lyases from Polysaccharide Lyase (PL) family 7 and a putative PL8 with similarity to ascomycete chondroitin AC lyases. Phylogenetic and homology analyses place the PL7 sequences amongst mannuronic acid specific PL7 proteins from marine bacteria. Recombinant expression, purification and characterization of one of the PL7 genes confirmed the specificity. Proteomic analysis of the P. salina secretome when growing on brown algae, revealed the PL7 and PL8 enzymes abundantly secreted together with enzymes necessary for degradation of laminarin, cellulose, lipids and peptides. Our findings indicate that the basic CAZyme repertoire of saprobic and plant pathogenic ascomycetes, with the addition of PL7 alginate lyases, provide P. salina with sufficient enzymatic capabilities to degrade several types of brown algae polysaccharides.

Highlights

Knowledge of the diversity and distribution of marine fungi is increasing in step with improvements in culture-based and molecular identification techniques and increased research efforts[1,2,3,4,5,6,7,8,9]
The annotation analysis of the P. salina genome revealed a repertoire of putative enzymes, which theoretically degrade the majority of the polysaccharides in brown algae, including alginate
The proteomic and genomic analysis of the CAZymes of P. salina strongly suggests that presence of the PL7 alginate lyases is one of the most significant adaptations of P. salina to thrive on brown macro-algae

Summary

Introduction

Knowledge of the diversity and distribution of marine fungi is increasing in step with improvements in culture-based and molecular identification techniques and increased research efforts[1,2,3,4,5,6,7,8,9]. Several reports investigating enzyme secretion and carbon utilization have confirmed the ability of P. salina to utilize alginate, laminarin and cellulose from brown algae[8,9]. Based on this we identified P. salina as an interesting candidate for studying potential adaptations of its enzyme repertoire to the breakdown of brown algae polysaccharides. By using a combination of genomics, culture-based methods and shotgun proteomics we show that P. salina secretes enzymes capable of catalyzing degradation of a range of polysaccharides found in brown macroalgae, notably alginate. Our study indicates that alginate lyase is the only additional enzyme adaptation necessary for allowing P. salina to degrade brown algae, when compared to its terrestrial relatives

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