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Integron gene cassettes: a repository of novel protein folds with distinct interaction sites
- Source :
- PLoS ONE, PLoS ONE, Vol 8, Iss 1, p e52934 (2013)
- Publication Year :
- 2012
-
Abstract
- Mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. In most cases, functional annotation of gene cassettes directly recovered by cassette-PCR is obscured by their characteristically high sequence novelty. This inhibits identification of those specific functions or biological features that might constitute preferential factors for lateral gene transfer via the integron system. A structural genomics approach incorporating x-ray crystallography has been utilised on a selection of cassettes to investigate evolutionary relationships hidden at the sequence level. Gene cassettes were accessed from marine sediments (pristine and contaminated sites), as well as a range of Vibrio spp. We present six crystal structures, a remarkably high proportion of our survey of soluble proteins, which were found to possess novel folds. These entirely new structures are diverse, encompassing all-α, α+β and α/β fold classes, and many contain clear binding pocket features for small molecule substrates. The new structures emphasise the large repertoire of protein families encoded within the integron cassette metagenome and which remain to be characterised. Oligomeric association is a notable recurring property common to these new integron-derived proteins. In some cases, the protein–protein contact sites utilised in homomeric assembly could instead form suitable contact points for heterogeneous regulator/activator proteins or domains. Such functional features are ideal for a flexible molecular componentry needed to ensure responsive and adaptive bacterial functions.
- Subjects :
- Models, Molecular
lcsh:Medicine
Integron
Crystallography, X-Ray
Biochemistry
Protein Structure, Secondary
Integrons
Protein structure
Biomacromolecule-Ligand Interactions
lcsh:Science
Peptide sequence
Vibrio cholerae
Oligonucleotide Array Sequence Analysis
Genetics
0303 health sciences
Multidisciplinary
biology
Genomics
Enzymes
Functional Genomics
Protein Classes
Horizontal gene transfer
Protein Binding
Research Article
Protein Structure
Protein family
Gene Transfer, Horizontal
Molecular Sequence Data
Sequence alignment
Computational biology
Microbiology
Structural genomics
Microbial Ecology
03 medical and health sciences
Bacterial Proteins
Amino Acid Sequence
Protein Interactions
Gene
Biology
030304 developmental biology
Binding Sites
030306 microbiology
lcsh:R
Proteins
Computational Biology
Genes, Bacterial
Enzyme Structure
Microbial Evolution
biology.protein
Metagenome
lcsh:Q
Structural Genomics
Metagenomics
Subjects
Details
- ISSN :
- 19326203
- Volume :
- 8
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- PloS one
- Accession number :
- edsair.doi.dedup.....bbb5d1694d9da2f1ca31ed861075fc64