Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland’s permafrost
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 sam...
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ftubristolcris:oai:research-information.bris.ac.uk:publications/e653ef40-2c32-4f3d-a220-bc218a08a112 2024-04-28T08:21:55+00:00 Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland’s permafrost Varliero, Gilda Rafiq, Muhammad Singh, Swati Summerfield, Annabel Sgouridis, Fotis Cowan, Donald Barker, Gary L A 2021-09-16 https://hdl.handle.net/1983/e653ef40-2c32-4f3d-a220-bc218a08a112 https://research-information.bris.ac.uk/en/publications/e653ef40-2c32-4f3d-a220-bc218a08a112 eng eng https://research-information.bris.ac.uk/en/publications/e653ef40-2c32-4f3d-a220-bc218a08a112 info:eu-repo/semantics/restrictedAccess Varliero , G , Rafiq , M , Singh , S , Summerfield , A , Sgouridis , F , Cowan , D & Barker , G L A 2021 , ' Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland’s permafrost ' , FEMS Microbiology Ecology . article 2021 ftubristolcris 2024-04-03T16:07:14Z 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. Article in Journal/Newspaper Greenland permafrost University of Bristol: Bristol Research |
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Open Polar |
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University of Bristol: Bristol Research |
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ftubristolcris |
language |
English |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Varliero, Gilda Rafiq, Muhammad Singh, Swati Summerfield, Annabel Sgouridis, Fotis Cowan, Donald Barker, Gary L A |
spellingShingle |
Varliero, Gilda Rafiq, Muhammad Singh, Swati Summerfield, Annabel Sgouridis, Fotis Cowan, Donald Barker, Gary L A Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland’s permafrost |
author_facet |
Varliero, Gilda Rafiq, Muhammad Singh, Swati Summerfield, Annabel Sgouridis, Fotis Cowan, Donald Barker, Gary L A |
author_sort |
Varliero, Gilda |
title |
Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland’s permafrost |
title_short |
Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland’s permafrost |
title_full |
Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland’s permafrost |
title_fullStr |
Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland’s permafrost |
title_full_unstemmed |
Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland’s permafrost |
title_sort |
microbial characterisation and cold-adapted predicted protein (capp) database construction from the active layer of greenland’s permafrost |
publishDate |
2021 |
url |
https://hdl.handle.net/1983/e653ef40-2c32-4f3d-a220-bc218a08a112 https://research-information.bris.ac.uk/en/publications/e653ef40-2c32-4f3d-a220-bc218a08a112 |
genre |
Greenland permafrost |
genre_facet |
Greenland permafrost |
op_source |
Varliero , G , Rafiq , M , Singh , S , Summerfield , A , Sgouridis , F , Cowan , D & Barker , G L A 2021 , ' Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland’s permafrost ' , FEMS Microbiology Ecology . |
op_relation |
https://research-information.bris.ac.uk/en/publications/e653ef40-2c32-4f3d-a220-bc218a08a112 |
op_rights |
info:eu-repo/semantics/restrictedAccess |
_version_ |
1797583940664426496 |