Evidence map›Paper›PMID 31015289›Full record

ArticleScience signaling2019

Tracing the origin and evolution of pseudokinases across the tree of life.

Annie Kwon, Steven Scott, Rahil Taujale, Wayland Yeung, Krys J Kochut, Patrick A Eyers, Natarajan Kannan

Open access · greenAbstract read
In one paragraph

Article in Science signaling, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.

0numbers the graph read from it
0cells of the map it votes in
61citing papers in PubMed
8.6field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

61 citing papers in PubMed, 125 citations in OpenAlex.

  1. Review
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  17. A conserved juxtamembrane motif in plant NFR5 receptors is essential for root nodule symbiosis.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  18. Article
  19. Article
  20. Article

1 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors at 2 institutions in 2 countries.

Annie KwonInstitute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.ORCID 0000-0002-2331-7575
Steven ScottDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.ORCID 0000-0002-4562-8729
Rahil TaujaleInstitute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.ORCID 0000-0003-1292-1619
Wayland YeungInstitute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.ORCID 0000-0002-2523-4984
Krys J KochutDepartment of Computer Science, University of Georgia, Athens, GA 30602, USA.
Patrick A EyersDepartment of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.ORCID 0000-0002-9220-2966
Natarajan KannanInstitute of Bioinformatics, University of Georgia, Athens, GA 30602, USA. nkannan@uga.edu.ORCID 0000-0002-2833-8375
University of Georgia · USUniversity of Liverpool · GB

Funding

Functional Annotation of Natural and Disease Variants in Tryosine KinasesR01GM114409 · NIGMS · UNIVERSITY OF GEORGIA · PI KANNAN, NATARAJAN · 2015 to 2020
$1.6M
Glycoscience Training ProgramT32GM107004 · NIGMS · UNIVERSITY OF GEORGIA · PI AMSTER, I JONATHAN, HALTIWANGER, ROBERT S. · 2014 to 2021
$1.3M
Biotechnology and Biological Sciences Research Council BB/N021703/1NIGMS NIH HHS R01 GM114409NIGMS NIH HHS T32 GM107004
6 · The paper itself

Abstract

Protein phosphorylation by eukaryotic protein kinases (ePKs) is a fundamental mechanism of cell signaling in all organisms. In model vertebrates, ~10% of ePKs are classified as pseudokinases, which have amino acid changes within the catalytic machinery of the kinase domain that distinguish them from their canonical kinase counterparts. However, pseudokinases still regulate various signaling pathways, usually doing so in the absence of their own catalytic output. To investigate the prevalence, evolutionary relationships, and biological diversity of these pseudoenzymes, we performed a comprehensive analysis of putative pseudokinase sequences in available eukaryotic, bacterial, and archaeal proteomes. We found that pseudokinases are present across all domains of life, and we classified nearly 30,000 eukaryotic, 1500 bacterial, and 20 archaeal pseudokinase sequences into 86 pseudokinase families, including ~30 families that were previously unknown. We uncovered a rich variety of pseudokinases with notable expansions not only in animals but also in plants, fungi, and bacteria, where pseudokinases have previously received cursory attention. These expansions are accompanied by domain shuffling, which suggests roles for pseudokinases in plant innate immunity, plant-fungal interactions, and bacterial signaling. Mechanistically, the ancestral kinase fold has diverged in many distinct ways through the enrichment of unique sequence motifs to generate new families of pseudokinases in which the kinase domain is repurposed for noncanonical nucleotide binding or to stabilize unique, inactive kinase conformations. We further provide a collection of annotated pseudokinase sequences in the Protein Kinase Ontology (ProKinO) as a new mineable resource for the signaling community.

Indexed as

Evolution, MolecularModels, GeneticModels, MolecularProtein KinasesProtein Kinases

Identifiers

PMID31015289
PMCPMC6997932
OpenAlexW2941880204

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.