Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost
dc.contributor.author | Varliero, Gilda | |
dc.contributor.author | Rafiq, Muhammad | |
dc.contributor.author | Singh, Swati | |
dc.contributor.author | Summerfield, Annabel | |
dc.contributor.author | Sgouridis, Fotis | |
dc.contributor.author | Cowan, Don A. | |
dc.contributor.author | Barker, Gary | |
dc.date.accessioned | 2022-08-30T09:52:04Z | |
dc.date.available | 2022-08-30T09:52:04Z | |
dc.date.issued | 2021-10 | |
dc.description.abstract | Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (>164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering. | en_US |
dc.description.department | Biochemistry | en_US |
dc.description.department | Genetics | en_US |
dc.description.department | Microbiology and Plant Pathology | en_US |
dc.description.librarian | hj2022 | en_US |
dc.description.sponsorship | The Natural Environment Research Council and the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant. | en_US |
dc.description.uri | http://femsec.oxfordjournals.org | en_US |
dc.identifier.citation | Gilda Varliero, Muhammad Rafiq, Swati Singh, Annabel Summerfield, Fotis Sgouridis, Don A Cowan, Gary Barker, Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost, FEMS Microbiology Ecology, Volume 97, Issue 10, October 2021, fiab127, https://doi.org/10.1093/femsec/fiab127. | en_US |
dc.identifier.issn | 0168-6496 (print) | |
dc.identifier.issn | 1574-6941 (online) | |
dc.identifier.other | 10.1093/femsec/fiab127 | |
dc.identifier.uri | https://repository.up.ac.za/handle/2263/86993 | |
dc.language.iso | en | en_US |
dc.publisher | Oxford University Press | en_US |
dc.rights | © The Author(s) 2021. Published by Oxford University Press on behalf of FEMS. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. | en_US |
dc.subject | Cold-adapted protein (CAPP) | en_US |
dc.subject | Bioengineering | en_US |
dc.subject | Soil metagenomics | en_US |
dc.subject | Soil metatranscriptomics | en_US |
dc.subject | Permafrost | en_US |
dc.subject | Greenland ice sheet (GrIS) | en_US |
dc.title | Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost | en_US |
dc.type | Article | en_US |
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