Evidence map›Paper›PMID 27238023›Full record

ArticleCell2016

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria.

Jason M Peters, Alexandre Colavin, Handuo Shi, Tomasz L Czarny, Matthew H Larson, Spencer Wong, John S Hawkins, Candy H S Lu, Byoung-Mo Koo, Elizabeth Marta and 7 more

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

Article in Cell, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 414 papers.

0numbers the graph read from it
0cells of the map it votes in
414citing papers in PubMed
75.1field-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

414 citing papers in PubMed, 772 citations in OpenAlex.

  1. The phenotypic landscape of the model firmicuteProceedings of the National Academy of Sciences of the United States of America · 2026
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  4. Markerless gene deletion inMicrobiology spectrum · 2026
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  7. Programmable genetic control of tumor-colonizingbioRxiv : the preprint server for biology · 2026
    Article
  8. Review
  9. Review
  10. Review
  11. Article
  12. Article
  13. DNA polymerase I: structure, activity, and function in bacterial DNA replication and repair.Critical reviews in biochemistry and molecular biology · 2026
    Review
  14. Article
  15. Article
  16. Article
  17. Article
  18. Systematic CRISPRi screening reveals genetic modulators ofbioRxiv : the preprint server for biology · 2026
    Article
  19. Article
  20. Article

354 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

17 authors at 5 institutions in 2 countries.

Jason M PetersDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
Alexandre ColavinBiophysics Program, Stanford University, Stanford, CA 94305, USA.
Handuo ShiDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Tomasz L CzarnyDepartment of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 3Z5, Canada; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada.
Matthew H LarsonDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Spencer WongDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
John S HawkinsDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA.
Candy H S LuDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
Byoung-Mo KooDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
Elizabeth MartaDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
Anthony L ShiverDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA.
Evan H WhiteheadDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
Jonathan S WeissmanDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA; UCSF Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
Eric D BrownDepartment of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 3Z5, Canada; Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada.
Lei S QiDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA. Electronic address: stanley.qi@stanford.edu.
Kerwyn Casey HuangBiophysics Program, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; School of Medicine, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. Electronic address: kchuang@stanford.edu.
Carol A GrossDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: cgrossucsf@gmail.com.
University of California, San Francisco · USStanford University · USMcMaster University · CAQB3 · USUniversity of California, Berkeley · US

Funding

TRAINING & OUTREACH COREP50GM107615 · NIGMS · STANFORD UNIVERSITY · PI TERUEL, MARY N · 2013 to 2017
$10.9M
STRUCTURAL BIOLOGY TRAINING PROGRAMT32GM008284 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KORTEMME, TANJA · 1988 to 2022
$10.1M
Cellular homeostasis pathways in bacteriaR35GM118061 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GROSS, CAROL ANNE · 2016 to 2025
$9.0M
Molecular Biophysics Training Program at StanfordT32GM008294 · NIGMS · STANFORD UNIVERSITY · PI HUANG, KERWYN C. · 1989 to 2019
$7.4M
Harnessing CRISPR for Targeted and Inducible Epigenomic ReprogrammingR01DA036858 · NIDA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LIM, WENDELL A, QI, LEI STANLEY · 2013 to 2017
$2.9M
Engineering of cell shape and intracellular organizationDP2OD006466 · OD · STANFORD UNIVERSITY · PI HUANG, KERWYN C. · 2009 to 2009
$2.4M
A novel RNA-guided platform for sequence-specific cell reprogrammingDP5OD017887 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI QI, LEI STANLEY · 2013 to 2017
$2.0M
Gene Function and Pathway Analysis Using Systems Level Approaches in ProkaryotesR01GM102790 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GROSS, CAROL ANNE · 2012 to 2015
$1.8M
Hi-resolution dynamic imaging of chromosomes in single cells by combined CRISPR imaging and sequential FISHU01EB021240 · NIBIB · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI CAI, LONG, QI, LEI STANLEY · 2015 to 2017
$1.4M
Systematic Phenotypic Analysis of the Gram-positive EnvelopeF32GM108222 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI PETERS, JASON M. · 2013 to 2016
$161k
NIBIB NIH HHS U01 EB021240NIDA NIH HHS R01 DA036858NIGMS NIH HHS F32 GM108222NIGMS NIH HHS P50 GM107615NIGMS NIH HHS R01 GM102790NIGMS NIH HHS R35 GM118061NIGMS NIH HHS T32 GM008284NIGMS NIH HHS T32 GM008294NIH HHS DP2 OD006466NIH HHS DP5 OD017887
6 · The paper itself

Abstract

Essential gene functions underpin the core reactions required for cell viability, but their contributions and relationships are poorly studied in vivo. Using CRISPR interference, we created knockdowns of every essential gene in Bacillus subtilis and probed their phenotypes. Our high-confidence essential gene network, established using chemical genomics, showed extensive interconnections among distantly related processes and identified modes of action for uncharacterized antibiotics. Importantly, mild knockdown of essential gene functions significantly reduced stationary-phase survival without affecting maximal growth rate, suggesting that essential protein levels are set to maximize outgrowth from stationary phase. Finally, high-throughput microscopy indicated that cell morphology is relatively insensitive to mild knockdown but profoundly affected by depletion of gene function, revealing intimate connections between cell growth and shape. Our results provide a framework for systematic investigation of essential gene functions in vivo broadly applicable to diverse microorganisms and amenable to comparative analysis.

Indexed as

Genes, BacterialGenes, EssentialBacillus subtilisCRISPR-Cas SystemsGene Knockdown TechniquesGene LibraryGene Regulatory NetworksMolecular Targeted Therapy

Identifiers

PMID27238023
PMCPMC4894308
OpenAlexW2407174002

What OpenQuestion holds

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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.