Evidence map›Paper›PMID 20833318›Full record

ReviewCurrent biology : CB2010

Hierarchical evolution of the bacterial sporulation network.

Michiel J L de Hoon, Patrick Eichenberger, Dennis Vitkup

Open access · bronzeAbstract readReview
In one paragraph

Review in Current biology : CB, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers.

0numbers the graph read from it
0cells of the map it votes in
120citing papers in PubMed
8.0field-weighted citation impact, top 2% 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

120 citing papers in PubMed, 224 citations in OpenAlex.

  1. Article
  2. Article
  3. Genome analysis and exploration ofFrontiers in microbiology · 2026
    Article
  4. Sporulation kinetics ofApplied and environmental microbiology · 2025
    Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Review
  11. Article
  12. Article
  13. Strategies for effective high pressure germination or inactivation ofApplied and environmental microbiology · 2024
    Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. The small acid-soluble proteins ofbioRxiv : the preprint server for biology · 2024
    Article
  20. Review

60 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

3 authors at 3 institutions in 2 countries.

Michiel J L de HoonCenter for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.
Patrick Eichenberger
Dennis Vitkup
Columbia University · USNew York University · USRIKEN Center for Integrative Medical Sciences · JP

Funding

Nation Center: Multi-Scale Study- Cellular Networks(RMI)U54CA121852 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2005 to 2015
$37.4M
Computational Annotation of Orphan Metabolic ActivitiesR01GM079759 · NIGMS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI VITKUP, DENNIS · 2007 to 2017
$3.2M
A multidisciplinary approach to elucidating gene function in a model Gram-positivRC2GM092616 · NIGMS · HARVARD MEDICAL SCHOOL · PI RUDNER, DAVID Z · 2009 to 2010
$2.0M
A systems level analysis of spore coat assembly in Bacillus subtilisR01GM081571 · NIGMS · NEW YORK UNIVERSITY · PI EICHENBERGER, PATRICK · 2008 to 2012
$1.5M
NCI NIH HHS U54 CA121852NCI NIH HHS U54CA121852NIGMS NIH HHS GM079759NIGMS NIH HHS GM081571NIGMS NIH HHS GM092616NIGMS NIH HHS R01 GM079759NIGMS NIH HHS R01 GM081571NIGMS NIH HHS RC2 GM092616
6 · The paper itself

Abstract

Genome sequencing of multiple species makes it possible to understand the main principles behind the evolution of developmental regulatory networks. It is especially interesting to analyze the evolution of well-defined model systems in which conservation patterns can be directly correlated with the functional roles of various network components. Endospore formation (sporulation), extensively studied in Bacillus subtilis, is driven by such a model bacterial network of cellular development and differentiation. In this review, we analyze the evolution of the sporulation network in multiple endospore-forming bacteria. Importantly, the network evolution is not random but primarily follows the hierarchical organization and functional logic of the sporulation process. Specifically, the sporulation sigma factors and the master regulator of sporulation, Spo0A, are conserved in all considered spore-formers. The sequential activation of these global regulators is also strongly conserved. The feed-forward loops, which are likely used to fine-tune waves of gene expression within regulatory modules, show an intermediate level of conservation. These loops are less conserved than the sigma factors but significantly more than the structural sporulation genes, which form the lowest level in the functional and evolutionary hierarchy of the sporulation network. Interestingly, in spore-forming bacteria, gene regulation is more conserved than gene presence for sporulation genes, while the opposite is true for non-sporulation genes. The observed patterns suggest that, by understanding the functional organization of a developmental network in a model organism, it is possible to understand the logic behind the evolution of this network in multiple related species.

Indexed as

Evolution, MolecularSpores, BacterialBacillus subtilisDNA ReplicationGene Regulatory NetworksPhylogenyTranscription, Genetic

Identifiers

PMID20833318
PMCPMC2944226
OpenAlexW2142322930

What OpenQuestion holds

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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.