Evidence map›Paper›PMID 29645342›Full record

ArticleProteomics2018

Identifying New Small Proteins in Escherichia coli.

Caitlin E VanOrsdel, John P Kelly, Brittany N Burke, Christina D Lein, Christopher E Oufiero, Joseph F Sanchez, Larry E Wimmers, David J Hearn, Fatimeh J Abuikhdair, Kathryn R Barnhart and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Proteomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.

0numbers the graph read from it
0cells of the map it votes in
42citing papers in PubMed
–field-weighted citation impact
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

42 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Analysis of stress-induced small proteins inbioRxiv : the preprint server for biology · 2025
    Article
  7. Article
  8. Review
  9. Article
  10. Article
  11. Article
  12. Article
  13. Article
  14. Review
  15. Article
  16. Article
  17. Article
  18. Review
  19. Article
  20. Rescue ofeLife · 2023
    Article
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

15 authors.

Caitlin E VanOrsdelDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.
John P KellyDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.ORCID 0000-0002-6430-0606
Brittany N BurkeDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.ORCID 0000-0002-0282-9846
Christina D LeinDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.
Christopher E OufieroDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.
Joseph F SanchezDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.ORCID 0000-0002-6357-2060
Larry E WimmersDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.
David J HearnDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.ORCID 0000-0002-2171-2002
Fatimeh J AbuikhdairDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.
Kathryn R BarnhartDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.
Michelle L DuleyDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.
Sarah E G ErnstDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.
Briana A KenersonDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.
Aubrey J SerafinDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.
Matthew R HemmDepartment of Biological Sciences, Smith Hall, Towson University, Towson, MD, USA.

Funding

Role of Small Transmembrane Proteins in Cytochrome bd Oxidase ActivityR15AI094548 · NIAID · TOWSON UNIVERSITY · PI HEMM, MATTHEW ROBERT · 2011 to 2011
$389k
NIAID NIH HHS R15 AI094548
6 · The paper itself

Abstract

The number of small proteins (SPs) encoded in the Escherichia coli genome is unknown, as current bioinformatics and biochemical techniques make short gene and small protein identification challenging. One method of small protein identification involves adding an epitope tag to the 3' end of a short open reading frame (sORF) on the chromosome, with synthesis confirmed by immunoblot assays. In this study, this strategy was used to identify new E. coli small proteins, tagging 80 sORFs in the E. coli genome, and assayed for protein synthesis. The selected sORFs represent diverse sequence characteristics, including degrees of sORF conservation, predicted transmembrane domains, sORF direction with respect to flanking genes, ribosome binding site (RBS) prediction, and ribosome profiling results. Of 80 sORFs, 36 resulted in encoded synthesized proteins-a 45% success rate. Modeling of detected versus non-detected small proteins analysis showed predictions based on RBS prediction, transcription data, and ribosome profiling had statistically-significant correlation with protein synthesis; however, there was no correlation between current sORF annotation and protein synthesis. These results suggest substantial numbers of small proteins remain undiscovered in E. coli, and existing bioinformatics techniques must continue to improve to facilitate identification.

Indexed as

Molecular Sequence AnnotationOpen Reading FramesProtein BiosynthesisComputational BiologyEscherichia coliEscherichia coli ProteinsGenome, BacterialRibosomesEscherichia coli Proteinssmall proteinsSPA-tagging

Identifiers

PMID29645342
PMCPMC6001520

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.