Evidence map›Paper›PMID 26873250›Full record

ArticleMolecular & cellular proteomics : MCP2016

Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported.

Maxim Shatsky, Simon Allen, Barbara L Gold, Nancy L Liu, Thomas R Juba, Sonia A Reveco, Dwayne A Elias, Ramadevi Prathapam, Jennifer He, Wenhong Yang and 17 more

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular & cellular proteomics : MCP, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
1.6field-weighted citation impact, top 17% 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

11 citing papers in PubMed, 25 citations in OpenAlex.

  1. Review
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  4. The DsrD functional marker protein is an allosteric activator of the DsrAB dissimilatory sulfite reductase.Proceedings of the National Academy of Sciences of the United States of America · 2022
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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

27 authors at 5 institutions in 1 country.

Maxim ShatskyFrom the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
Simon Allenthe Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143;
Barbara L Goldthe Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
Nancy L Liuthe Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
Thomas R Jubathe Departments of Biochemistry and of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, 65211;
Sonia A RevecoFrom the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
Dwayne A Eliasthe Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831;
Ramadevi Prathapamthe Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
Jennifer Hethe Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
Wenhong Yangthe Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
Evelin D Szakalthe Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143;
Haichuan Liuthe Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143;
Mary E Singerthe Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
Jil T Gellerthe Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
Bonita R Lamthe Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
Avneesh Sainithe Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
Valentine V Trotterthe Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
Steven C Hallthe Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143;
Susan J Fisherthe Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143;
Steven E BrennerFrom the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; the Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California, 94720;
Swapnil R ChhabraFrom the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
Terry C Hazenthe Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, 37996; and.
Judy D Wallthe Departments of Biochemistry and of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, 65211;
H Ewa Witkowskathe Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143;
Mark D Bigginthe Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720.
John-Marc ChandoniaFrom the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; gpbutland@lbl.gov jmchandonia@lbl.gov.
Gareth Butlandthe Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; gpbutland@lbl.gov jmchandonia@lbl.gov.
Lawrence Berkeley National Laboratory · USUniversity of California System · USUniversity of Missouri · USOak Ridge National Laboratory · USUniversity of Tennessee at Knoxville · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Numerous affinity purification-mass spectrometry (AP-MS) and yeast two-hybrid screens have each defined thousands of pairwise protein-protein interactions (PPIs), most of which are between functionally unrelated proteins. The accuracy of these networks, however, is under debate. Here, we present an AP-MS survey of the bacterium Desulfovibrio vulgaris together with a critical reanalysis of nine published bacterial yeast two-hybrid and AP-MS screens. We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli Compared with the nine published interactomes, our two networks are smaller, are much less highly connected, and have significantly lower false discovery rates. In addition, our interactomes are much more enriched in protein pairs that are encoded in the same operon, have similar functions, and are reproducibly detected in other physical interaction assays than the pairs reported in prior studies. Our work establishes more stringent benchmarks for the properties of protein interactomes and suggests that bona fide PPIs much more frequently involve protein partners that are annotated with similar functions or that can be validated in independent assays than earlier studies suggested.

Indexed as

Bacterial ProteinsChromatography, AffinityComputational BiologyDatabases, ProteinDesulfovibrio vulgarisEscherichia coliMass SpectrometryProtein Interaction MappingProtein Interaction MapsProteomicsTwo-Hybrid System TechniquesBacterial Proteins

Identifiers

PMID26873250
PMCPMC4858938
OpenAlexW2311515855

What OpenQuestion holds

Textmetadata
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.