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.
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|
dc.contributor.author |
Barker, Gary
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|
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 |