A proposed update for the classification and description of bacterial lipolytic enzymes
A peer-reviewed article of this Preprint also exists.
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Abstract
Bacterial lipolytic enzymes represent an important class of proteins: they provide their host species with access to additional resources and have multiple applications within the biotechnology sector. Since the formalisation of lipolytic enzymes into families and subfamilies, advances in molecular biology have led to the discovery of lipolytic enzymes unable to be classified via the existing system. Utilising sequence-based comparison methods, we have integrated these novel families within the classification system proposed by Arpigny and Jaeger (1999) and recently updated by Kovacic et al (2019) so that it now consists of 35 families and 11 true lipase subfamilies. Representative sequences for each family and subfamily have been defined as well as methodology for accurate comparison of novel sequences against the reference proteins, facilitating the future assignment of novel proteins. Both the code and protein sequences required for integration of additional families are available at: https://github.com/thh32/Lipase_reclassification
Cite this as
2019. A proposed update for the classification and description of bacterial lipolytic enzymes. PeerJ Preprints 7:e27725v1 https://doi.org/10.7287/peerj.preprints.27725v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a submission to PeerJ for review.
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Supplemental Information
Similarity of reported novel lipolytic proteins against the accepted type proteins for each lipolytic family
Both enzymes and the similarity scores of interest are in bold when high (>60%) similarity was identified.
Pairwise comparison of similarity between novel lipolytic proteins
Both enzymes and the similarity scores of interest are in bold when high (>60%) similarity was identified.
Annotation of each studied lipolytic protein against the genome database
For each protein its publication date and isolation source were reported. Genome annotation was conducted at two levels of strictness and taxonomy of matches reported at both the family and genus level. Taxonomy was assigned using both the NCBI taxonomic assignments and the GTDB method.
BLAST based assignment of taxonomy for lipolytic enzymes without a genome match
For each protein the top 10 sequence matches reported against the NR database are reported, including the source organism for each matching sequence.
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Thomas C A Hitch conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Thomas Clavel prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Data Deposition
The following information was supplied regarding data availability:
Funding
TC received funding from the German Research Foundation (DFG) (grant no. CL481/2-1). TCAH received internal funding from the START grant program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
