Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost

dc.contributor.authorVarliero, Gilda
dc.contributor.authorRafiq, Muhammad
dc.contributor.authorSingh, Swati
dc.contributor.authorSummerfield, Annabel
dc.contributor.authorSgouridis, Fotis
dc.contributor.authorCowan, Don A.
dc.contributor.authorBarker, Gary
dc.date.accessioned2022-08-30T09:52:04Z
dc.date.available2022-08-30T09:52:04Z
dc.date.issued2021-10
dc.description.abstractPermafrost 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.departmentBiochemistryen_US
dc.description.departmentGeneticsen_US
dc.description.departmentMicrobiology and Plant Pathologyen_US
dc.description.librarianhj2022en_US
dc.description.sponsorshipThe 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.urihttp://femsec.oxfordjournals.orgen_US
dc.identifier.citationGilda 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.issn0168-6496 (print)
dc.identifier.issn1574-6941 (online)
dc.identifier.other10.1093/femsec/fiab127
dc.identifier.urihttps://repository.up.ac.za/handle/2263/86993
dc.language.isoenen_US
dc.publisherOxford University Pressen_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.subjectCold-adapted protein (CAPP)en_US
dc.subjectBioengineeringen_US
dc.subjectSoil metagenomicsen_US
dc.subjectSoil metatranscriptomicsen_US
dc.subjectPermafrosten_US
dc.subjectGreenland ice sheet (GrIS)en_US
dc.titleMicrobial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrosten_US
dc.typeArticleen_US

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