Update on cpnDB: a reference database of chaperonin sequences

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Abstract

cpnDB was established in 2004 to provide a manually curated database of type I (60 kDa chaperonin, CPN60, also known as GroEL or HSP60) and type II (CCT, TRiC, thermosome) chaperonin sequences and to support chaperonin sequence-based applications including microbial species identification, detection and quantification, phylogenetic investigations and microbial community profiling. Since its establishment, cpnDB has grown to over 25 000 sequence records including over 4 000 records from bacterial type strains. The updated cpnDB webpage ( www.cpndb.ca) provides tools for text- or sequence-based searches and links to protocols, and selected reference data sets are available for download. Here we present an updated description of the contents and taxonomic coverage of cpnDB and an analysis of cpn60 sequence diversity.

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Most cited references 31

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Improved tools for biological sequence comparison.

W R Pearson, D J Lipman (1988)

We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment algorithm; these local similarities can be displayed as a "graphic matrix" plot or as individual alignments. In addition, these programs have been generalized to allow comparison of DNA or protein sequences based on a variety of alternative scoring matrices.

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Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies.

Rebecca J Case, Yan Boucher, Ingela Dahllöf … (2007)

Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identification of multiple ribotypes for a single organism. To evaluate the impact of such intragenomic heterogeneity on the performance of the 16S rRNA gene as a molecular marker, we compared its phylogenetic and evolutionary characteristics to those of the single-copy gene rpoB. Full-length gene sequences and gene fragments commonly used for denaturing gradient gel electrophoresis were compared at various taxonomic levels. Heterogeneity found between intragenomic 16S rRNA gene copies was concentrated in specific regions of rRNA secondary structure. Such "heterogeneity hot spots" occurred within all gene fragments commonly used in molecular microbial ecology. This intragenomic heterogeneity influenced 16S rRNA gene tree topology, phylogenetic resolution, and operational taxonomic unit estimates at the species level or below. rpoB provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoB could complement the information provided by the 16S rRNA gene.

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Two families of chaperonin: physiology and mechanism.

George W. Farr, Eli Chapman, Arthur L. Horwich … (2006)

Chaperonins are large ring assemblies that assist protein folding to the native state by binding nonnative proteins in their central cavities and then, upon binding ATP, release the substrate protein into a now-encapsulated cavity to fold productively. Two families of such components have been identified: type I in mitochondria, chloroplasts, and the bacterial cytosol, which rely on a detachable "lid" structure for encapsulation, and type II in archaea and the eukaryotic cytosol, which contain a built-in protrusion structure. We discuss here a number of issues under current study. What is the range of substrates acted on by the two classes of chaperonin, in particular by GroEL in the bacterial cytoplasm and CCT in the eukaryotic cytosol, and are all these substrates subject to encapsulation? What are the determinants for substrate binding by the type II chaperonins? And is the encapsulated chaperonin cavity a passive container that prevents aggregation, or could it be playing an active role in polypeptide folding?

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Journal

Journal ID (nlm-ta): Database (Oxford)

Journal ID (iso-abbrev): Database (Oxford)

Journal ID (publisher-id): databa

Title: Database: The Journal of Biological Databases and Curation

Publisher: Oxford University Press

ISSN (Electronic): 1758-0463

Publication date Collection: 2019

Publication date (Electronic): 01 March 2019

Publication date PMC-release: 01 March 2019

Volume: 2019

Electronic Location Identifier: baz033

Affiliations

[1]Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon SK, Canada

Author notes

Corresponding author: Tel: (306) 966-7242; Fax: (306) 966-7244; Email: Janet.Hill@ 123456usask.ca

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Janet E Hill http://orcid.org/0000-0002-2187-6277

Article

Publisher ID: baz033

DOI: 10.1093/database/baz033

PMC ID: 6395794

PubMed ID: 30820575

SO-VID: 3e12c7dd-7c0f-45e9-b548-7940cc79506e

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date received : 22 January 2019

Date revision received : 14 February 2019

Date accepted : 16 February 2019

Page count

Pages: 7

Funding

Funded by: Natural Sciences and Engineering Research Council of Canada 10.13039/501100000038

Update on cpnDB: a reference database of chaperonin sequences

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Most cited references 31

Improved tools for biological sequence comparison.

Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies.

Two families of chaperonin: physiology and mechanism.

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