title: The discovery of novel LPMO families with a new Hidden Markov model.
abstract: BACKGROUND
  Renewable biopolymers, such as cellulose, starch and chitin are highly resistance to enzymatic degradation. Therefore, there is a need to upgrade current degradation processes by including novel enzymes. Lytic polysaccharide mono-oxygenases (LPMOs) can disrupt recalcitrant biopolymers, thereby enhancing hydrolysis by conventional enzymes. However, novel LPMO families are difficult to identify using existing methods. Therefore, we developed a novel profile Hidden Markov model (HMM) and used it to mine genomes of ascomycetous fungi for novel LPMOs.
  
  
  RESULTS
  We constructed a structural alignment and verified that the alignment was correct. In the alignment we identified several known conserved features, such as the histidine brace and the N/Q/E-X-F/Y motif and previously unidentified conserved proline and glycine residues. These residues are distal from the active site, suggesting a role in structure rather than activity. The multiple protein alignment was subsequently used to build a profile Hidden Markov model. This model was initially tested on manually curated datasets and proved to be both sensitive (no false negatives) and specific (no false positives). In some of the genomes analyzed we identified a yet unknown LPMO family. This new family is mostly confined to the phyla of Ascomycota and Basidiomycota and the class of Oomycota. Genomic clustering indicated that at least some members might be involved in the degradation of β-glucans, while transcriptomic data suggested that others are possibly involved in the degradation of pectin.
  
  
  CONCLUSIONS
  The newly developed profile hidden Markov Model was successfully used to mine fungal genomes for a novel family of LPMOs. However, the model is not limited to bacterial and fungal genomes. This is illustrated by the fact that the model was also able to identify another new LPMO family in Drosophila melanogaster. Furthermore, the Hidden Markov model was used to verify the more distant blast hits from the new fungal family of LPMOs, which belong to the Bivalves, Stony corals and Sea anemones. So this Hidden Markov model (Additional file 3) will help the broader scientific community in identifying other yet unknown LPMOs.
authors.affiliation: Molecular Microbiology and Health, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
authors.forename: Gerben P
authors.initials: GP
authors.lastname: Voshol
authors.affiliation: Molecular Microbiology and Health, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
authors.forename: Erik
authors.initials: E
authors.lastname: Vijgenboom
authors.affiliation: Molecular Microbiology and Health, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands. peter.punt@ddna-biotech.com.|Dutch DNA Biotech B.V., Utrechtseweg 48, 3703HE, Zeist, The Netherlands. peter.punt@ddna-biotech.com.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Punt
mesh_terms: D020816:Amino Acid Motifs; D000818:Animals; D001203:Ascomycota / Q000145:classification / Q000201:enzymology / Q000235:genetics; D001487:Basidiomycota / Q000145:classification / Q000201:enzymology / Q000235:genetics; D001673:Biodegradation, Environmental; D049872:Bivalvia / Q000201:enzymology / Q000235:genetics; D002482:Cellulose / Q000378:metabolism; D002686:Chitin / Q000378:metabolism; D057225:Data Mining; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism; D004331:Drosophila melanogaster / Q000201:enzymology / Q000235:genetics; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism*; D016681:Genome, Fungal; D006868:Hydrolysis; D008390:Markov Chains; D006899:Mixed Function Oxygenases / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D009868:Oomycetes / Q000145:classification / Q000201:enzymology / Q000235:genetics; D010802:Phylogeny; D012615:Sea Anemones / Q000201:enzymology / Q000235:genetics; D016415:Sequence Alignment; D013213:Starch / Q000378:metabolism
chemical_list: D029721:Drosophila Proteins; D005656:Fungal Proteins; D002686:Chitin; D002482:Cellulose; D013213:Starch; D006899:Mixed Function Oxygenases
keywords: Fungi; Genome mining; Hidden Markov model, HMM; LPMO; Lytic polysaccharide mono-oxygenases; Pectin; β-Glucan