cpnDB Frequently Asked Questions

Vancuren SJ and Hill JE. 2019. Update on cpnDB: a reference database of chaperonin sequences. Database 2019:baz033 doi:10.1093/database/baz033.

Hill JE, Penny SL, Crowell KG, Goh SH and Hemmingsen SM. 2004. cpnDB: a chaperonin sequence database. Genome Res. 14:1669-1675.

Chaperonins are a diverse family of molecular chaperones that are present in the plastids, mitochondria, and cytoplasm of eukaryotes, eubacteria and archaea.

Group I chaperonins (CPN60) include mitochondrial and chloroplast proteins of approximately 60 kDa, which function in a tetradecameric, double-torus-shaped complex consisting of either 1 or 2 subunit types. Typically, they function as a pair of stacked rings, each containing 7 subunits, although there is evidence that single rings may be functional. Plastid CPN60 appears to be distinct from homologous proteins in bacteria and mitochondria in that it is composed of 2 distinct subunit types, alpha and beta. Group I chaperonins function with a cochaperonin protein (CPN10 or CPN21). GroEL and Hsp60 are synonyms of CPN60.

Group II chaperonins (CCT, for chaperonin containing TCP1 or TriC, for TCP1 ring complex) are archaeal and eukaryote cytoplasmic counterparts of the group I chaperonins. They consist of double-torus complexes of 16 subunits which, in eukaryotes, are composed of 8 subunit types. Archaeal group II chaperonin complexes are composed of variable numbers (often 2 or 3) of subunit types. Although no cochaperonin has been found to be required for group II chaperonin function, a protein cofactor, prefoldin (PFD), has been identified.

Many of the sequences in cpnDB are partial gene sequences, representing only the universal target portion of the cpn60 gene (group I chaperonin). An analysis of the cpn60 sequences from a variety of bacterial and eukaryotic species led to the design of universal, degenerate PCR primers which can be applied for the amplification of a 549-567 bp region of cpn60 corresponding to nucleotides 274-828 of the E. coli cpn60 sequence from virtually any genome (Goh et al. 1996). The utility of this cpn60 "universal target" (UT) for discriminating closely related bacterial species has been established and it has been demonstrated that the cpn60 UT region generally provides more discriminating and phylogenetically informative data than the 16S rDNA target (Brousseau et al. 2001). The cpn60 UT has also been employed as a target for sequence-based microbial ecology studies (Hill et al. 2002).

As with any "rule" of biology, as more and more data becomes available, exceptions occur. To date, several species of Mycoplasma (capricolum, mobile, mycoides, pulmonis, and synoviae) and Ureaplasma parvum have been found to lack type I chaperonin genes as well as other genes previously considered essential for prokaryotic life. All of these organisms are obligate intracellular species. Interestingly, eight species of Mycoplasma and Candidatus Carsonella ruddii, which has the smallest genome recognized to date (~160 kb), do have a type I chaperonin genes. These inconsistencies are perhaps best illustrated by Mycoplasma hyopneumoniae where 2 of the strains completely sequenced are missing cpn60 genes, while 1 strain (strain J) has a cpn60 gene.

Yes. cpn60 UT based phylogenies are consistent with those based on 16S rRNA, but cpn60 UT sequences are generally more variable, providing better resolution of closely related taxa. Links et al. (2012) used the Barcode of Life framework and criteria to establish that cpn60 UT is a preferred barcode for Bacteria compared to the 16S rRNA gene or its variable regions. Additional publications demonstrating the resolving power of the cpn60 UT are listed on the cpnDB publications page.

Full-length cpn60 sequences are available for only a subset of the species represented in cpnDB. Many of the sequences were determined through application of the universal, degenerate primers for cpn60 amplification so that only the universal target sequence is available.

Until 2003 (Klunker et al. 2003), Archaea were thought to possess Group II chaperonins only. Group II chaperonin sequences cannot be amplified with the universal, degenerate cpn60 primers and so there is no region of the Group II sequence corresponding to the Group I chaperonin universal target. For archaeal species with both Group I (cpn60) and Group II chaperonins, universal target sequences are included for the Group I (cpn60) genes.

We have developed a set of universal primers for the amplification of a region of the Group II chaperonin genes of Archaea. The amplified region corresponds to nucleotides 142-858 of the Group II chaperonin (alpha subunit) of Methanococcus maripaludis strain S2. As observed for the cpn60 UT, the thermosome target provides more discriminating information for closely related species than 16S rRNA. Details about these primers and associated applications can be found in Chaban & Hill (2011) ISME Journal 6:430-439, or on the Hill Lab Homepage.

cpnDB does not accept direct submissions of chaperonin sequence data. Instead, we encourage you to submit your chaperonin sequence data to one of the major public sequence databases (EMBL, NCBI, or DDBJ.) We survey these resources weekly for new chaperonin sequence data for incorporation into cpnDB.

Information about primers and protocols can be found on the Hill Lab Homepage or in relevant publications.