Abstract
BackgroundLytic polysaccharide monooxygenases are important enzymes for the decomposition of recalcitrant biological macromolecules such as plant cell wall and chitin polymers. These enzymes were originally designated glycoside hydrolase family 61 and carbohydrate-binding module family 33 but are now classified as auxiliary activities 9, 10 and 11 in the CAZy database. To obtain a systematic analysis of the divergent families of lytic polysaccharide monooxygenases we used Peptide Pattern Recognition to divide 5396 protein sequences resembling enzymes from families AA9 (1828 proteins), AA10 (2799 proteins) and AA11 (769 proteins) into subfamilies.ResultsThe results showed that the lytic polysaccharide monooxygenases have two conserved regions identified by conserved peptides specific for each AA family. The peptides were used for in silico PCR discovery of the lytic polysaccharide monooxygenases in 79 fungal and 95 bacterial genomes. The bacterial genomes encoded 0 – 7 AA10s (average 0.6). No AA9 or AA11 were found in the bacteria. The fungal genomes encoded 0 – 40 AA9s (average 7) and 0 – 15 AA11s (average 2) and two of the fungi possessed a gene encoding a putative AA10. The AA9s were mainly found in plant cell wall-degrading asco- and basidiomycetes in agreement with the described role of AA9 enzymes. In contrast, the AA11 proteins were found in 36 of the 39 ascomycetes and in only two of the 32 basidiomycetes and their abundance did not correlate to the degradation of cellulose and hemicellulose.ConclusionsThese results provides an overview of the sequence characteristics and occurrence of the divergent AA9, AA10 and AA11 families and pave the way for systematic investigations of the of lytic polysaccharide monooxygenases and for structure-function studies of these enzymes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1601-6) contains supplementary material, which is available to authorized users.
Highlights
Lytic polysaccharide monooxygenases are important enzymes for the decomposition of recalcitrant biological macromolecules such as plant cell wall and chitin polymers
This approach increases the risk of including non-lytic polysaccharide monooxygenases (LPMOs) proteins in the analysis we have previously found that Peptide Pattern Recognition (PPR) analysis separates unrelated proteins into different subfamilies [24,30]
To obtain as comprehensive sequence information about the LPMOs as possible we included the AA9, AA10 and AA11 sequences listed in the CAZy database in the PPR analysis and a wide selection of LPMOlike sequences found by similarity search in GenBank
Summary
Lytic polysaccharide monooxygenases are important enzymes for the decomposition of recalcitrant biological macromolecules such as plant cell wall and chitin polymers. These enzymes were originally designated glycoside hydrolase family 61 and carbohydrate-binding module family 33 but are classified as auxiliary activities 9, 10 and 11 in the CAZy database. Copper-dependent lytic polysaccharide monooxygenases (LPMOs) are important enzymes for degradation of biological macromolecules such as plant cell wall and chitin polymers [1,2,3,4,5,6]. The LPMOs were originally classified as glycoside hydrolases (GHs) and carbohydrate-binding modules (CBMs) but are placed in the auxiliary activity families AA9, AA10 and AA11 in the CAZy database [14]. Certain AA9 family members enhance enzymatic degradation of cellulose [3] and are important industrial enzymes for conversion of lignocellulotic biomass into soluble sugars
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