ArticleBMC genomics2011
Filtering "genic" open reading frames from genomic DNA samples for advanced annotation.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 27 citations in OpenAlex.
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- An efficient ORF selection system for DNA fragment libraries based on split beta-lactamase complementation.PloS one · 2020Article
- Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing.Journal of visualized experiments : JoVE · 2018Article
- Systematic autoantigen analysis identifies a distinct subtype of scleroderma with coincident cancer.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Mining gut microbiome oligopeptides by functional metaproteome display.Scientific reports · 2016Article
- Solution structure of a soluble fragment derived from a membrane protein by shotgun proteolysis.Protein engineering, design & selection : PEDS · 2015Article
- Identification of novel proteins binding the AU-rich element of α-prothymosin mRNA through the selection of open reading frames (RIDome).RNA biology · 2015Article
- An Air-Well sparging minifermenter system for high-throughput protein production.Microbial cell factories · 2014Article
- Library methods for structural biology of challenging proteins and their complexes.Current opinion in structural biology · 2013Review
- A novel helper phage enabling construction of genome-scale ORF-enriched phage display libraries.PloS one · 2013Article
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn order to carry out experimental gene annotation, DNA encoding open reading frames (ORFs) derived from real genes (termed "genic") in the correct frame is required. When genes are correctly assigned, isolation of genic DNA for functional annotation can be carried out by PCR. However, not all genes are correctly assigned, and even when correctly assigned, gene products are often incorrectly folded when expressed in heterologous hosts. This is a problem that can sometimes be overcome by the expression of protein fragments encoding domains, rather than full-length proteins. One possible method to isolate DNA encoding such domains would to "filter" complex DNA (cDNA libraries, genomic and metagenomic DNA) for gene fragments that confer a selectable phenotype relying on correct folding, with all such domains present in a complex DNA sample, termed the "domainome".
resultsIn this paper we discuss the preparation of diverse genic ORF libraries from randomly fragmented genomic DNA using ß-lactamase to filter out the open reading frames. By cloning DNA fragments between leader sequences and the mature ß-lactamase gene, colonies can be selected for resistance to ampicillin, conferred by correct folding of the lactamase gene. Our experiments demonstrate that the majority of surviving colonies contain genic open reading frames, suggesting that ß-lactamase is acting as a selectable folding reporter. Furthermore, different leaders (Sec, TAT and SRP), normally translocating different protein classes, filter different genic fragment subsets, indicating that their use increases the fraction of the "domainone" that is accessible.
conclusionsThe availability of ORF libraries, obtained with the filtering method described here, combined with screening methods such as phage display and protein-protein interaction studies, or with protein structure determination projects, can lead to the identification and structural determination of functional genic ORFs. ORF libraries represent, moreover, a useful tool to proceed towards high-throughput functional annotation of newly sequenced genomes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.