High-resolution protein–protein interaction mapping using all-versus-all sequencing (AVA-Seq) Article Swipe
Simeon Andrews
,
Stephanie Schaefer‐Ramadan
,
Nayra M. Al‐Thani
,
Ikhlak Ahmed
,
Yasmin A. Mohamoud
,
Joel A. Malek
·
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1074/jbc.ra119.008792
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1074/jbc.ra119.008792
Two-hybrid systems can be used for investigating protein-protein interactions and may provide important information about gene products with unknown function. Despite their success in mapping protein interactions, two-hybrid systems have remained mostly untouched by improvements in next-generation DNA sequencing. The two-hybrid systems rely on one-versus-all methods in which each bait is sequentially screened against an entire library. Here, we developed a screening method that joins both bait and prey as a convergent fusion into one bacterial plasmid vector that can then be amplified and paired-end sequencing by next-generation sequencing (NGS). Our method enables all-versus-all sequencing (AVA-Seq) and utilizes NGS to remove multiple bottlenecks of the two-hybrid system. AVA-Seq allows for high-resolution protein-protein interaction mapping of a small set of proteins and has the potential for lower-resolution mapping of entire proteomes. Features of the system include ORF selection to improve efficiency, high bacterial transformation efficiency, a convergent fusion vector to allow paired-end sequencing of interactors, and the use of protein fragments rather than full-length proteins to better resolve specific protein contact points. We demonstrate the system's strengths and limitations on a set of proteins known to interact in humans and provide a framework for future large-scale projects.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1074/jbc.ra119.008792
- http://www.jbc.org/article/S0021925820306578/pdf
- OA Status
- hybrid
- Cited By
- 14
- References
- 19
- Related Works
- 10
- OpenAlex ID
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All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2950227120Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1074/jbc.ra119.008792Digital Object Identifier
- Title
-
High-resolution protein–protein interaction mapping using all-versus-all sequencing (AVA-Seq)Work title
- Type
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articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2019Year of publication
- Publication date
-
2019-06-10Full publication date if available
- Authors
-
Simeon Andrews, Stephanie Schaefer‐Ramadan, Nayra M. Al‐Thani, Ikhlak Ahmed, Yasmin A. Mohamoud, Joel A. MalekList of authors in order
- Landing page
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https://doi.org/10.1074/jbc.ra119.008792Publisher landing page
- PDF URL
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https://www.jbc.org/article/S0021925820306578/pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
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hybridOpen access status per OpenAlex
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https://www.jbc.org/article/S0021925820306578/pdfDirect OA link when available
- Concepts
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Computational biology, Biology, Protein function, DNA sequencing, Function (biology), Proteome, Transformation (genetics), Genetics, Gene, Computer scienceTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
14Total citation count in OpenAlex
- Citations by year (recent)
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2025: 2, 2024: 1, 2023: 2, 2022: 4, 2021: 4Per-year citation counts (last 5 years)
- References (count)
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19Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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