Chaperonins are a diverse family of molecular chaperones present in the plastids, mitochondria, and cytoplasm of eukaryotes, bacteria and archaea. The family is divided into group I (CPN60, also known as Hsp60 or GroEL, found in bacteria, some archaea, mitochondria and plastids) and group II (CCT, TriC or thermosome, found in archaea and the eukaryotic cytoplasm).
Group I chaperonin sequences have been employed as targets for detection and identification of organisms and microbiome studies since a 549-567 bp segment of the cpn60 coding region is a molecular barcode that can be amplified with universal PCR primers.
Species level identification of bacteria can be achieved with as little as 150 bp of the cpn60 barcode.
The goal of the cpnDB project is to provide a manually curated, taxonomically broad collection of chaperonin sequences.
cpnDB downloads Reference cpn60 barcodes sequences (FASTA) and metadata for use in your own workflows.
cpn60-Classifier (Github) This repository contains training sequences and taxonomy information that can be used with the QIIME2 q2-feature-classifier plugin to taxonomically assign cpn60 sequences.
cpn60 barcoding protocols from the Hill Lab for microbiome studies or identification of individual isolates.
References
Ren, Q. and Hill, J.E.* 2023. Rapid and accurate taxonomic classification of cpn60 amplicon sequence variants. ISME Communications, 3:77 doi.org/10.1038/s43705-023-00283-z
Vancuren, S.J. and Hill, J.E. 2019. Update on cpnDB: a reference database of chaperonin sequences. Database, 2019, doi:10.1093/database/baz033
Hill, J.E., Penny, S.L., Crowell, K.G., Goh, S.H. and Hemmingsen, S.M. 2004. cpnDB: a chaperonin sequence database. Genome Research 14:1669-1675. doi:10.1101/gr.2649204
