The circadian clock and darkness control natural competence in cyanobacteria
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Abstract
The cyanobacterium Synechococcus elongatus is a model organism for the study of circadian rhythms. It is naturally competent for transformation-that is, it takes up DNA from the environment, but the underlying mechanisms are unclear. Here, we use a genome-wide screen to identify genes required for natural transformation in S. elongatus, including genes encoding a conserved Type IV pilus, genes known to be associated with competence in other bacteria, and others. Pilus biogenesis occurs daily in the morning, while natural transformation is maximal when the onset of darkness coincides with the dusk circadian peak. Thus, the competence state in cyanobacteria is regulated by the circadian clock and can adapt to seasonal changes of day length.
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Synechococcus elongatus PCC 7942 is naturally competent and can undergo natural transformation; DNA can be introduced as replicative plasmids, integrative plasmids, or linear PCR fragments; when introduced DNA contains regions homologous to the chromosome, it can integrate into defined neutral sites through homologous recombination, enabling stable gene insertion, deletion, or replacement.
“Like Synechocystis sp. PCC 6803, Synechococcus elongatus PCC 7942 is naturally competent and can undergo natural transformation, whereby extracellular DNA is taken up directly from the surrounding medium. In this strain, DNA can be introduced as replicative plasmids, integrative plasmids, or linear PCR fragments; when the introduced DNA contains regions homologous to the chromosome, it can”
From Cyanobacteria as a Photosynthetic Chassis for Metabolic Pathway Engineering with Heterologous Gene Expression (2026) · cites this paper as [61]
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Experimental — accuracy not yet measuredConjugation from E. coli provides an additional route for delivering transferable or broad-host-range plasmids to S. elongatus PCC 7942, while electroporation is less routinely used.
“Conjugation from E. coli provides an additional route for delivering transferable or broad-host-range plasmids, while electroporation has been reported for cyanobacteria but is less routinely used for S. elongatus PCC 7942 [61].”
From Cyanobacteria as a Photosynthetic Chassis for Metabolic Pathway Engineering with Heterologous Gene Expression (2026) · cites this paper as [61]
The Introduction mentions conjugation only as a general route of genetic exchange. The Methods section “Strains, plasmids, and molecular methods” describes natural transformation of S. elongatus and propagation of plasmids in E. coli, but not conjugative delivery between them. Searches for electroporation found no passage addressing its use or how routinely it is used. (LLM, conf=0.76)
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Additional file 1 of Time of day as a critical variable in biology
Nelson, R. J., Bumgarner, J. R., Liu, J. A., Love, J. A., Meléndez‐Fernández, O. H., Becker‐Krail, D. D., Walker, W. H., Walton, J. C., DeVries, A. C., & Prendergast, B. J. (2022) · Figshare · doi:10.6084/m9.figshare.20076774
Additional file 2 of Time of day as a critical variable in biology
Nelson, R. J., Bumgarner, J. R., Liu, J. A., Love, J. A., Meléndez‐Fernández, O. H., Becker‐Krail, D. D., Walker, W. H., Walton, J. C., DeVries, A. C., & Prendergast, B. J. (2022) · Figshare · doi:10.6084/m9.figshare.20076777
Diel transcriptional dynamics of a marine sponge and its microbiome in a natural environment
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Distinct core minor pilin complexes prime specialized type IV filaments in cyanobacteriaPreprint
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Calcium signals natural transformation in Acinetobacter baumanniiPreprint
Chirakadavil, J. B., Goldlust, K., Poiré, L., Nc, G., Chassard, A., Camilli, A., Bouvier, M., Laaberki, M.-H., & Charpentier, X. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.23.707608
Llop, A., Tremiño, L., & Contreras, A. (2026) · Scientific Reports · doi:10.1038/s41598-026-43837-6
- Authors
- Taton, A., Erikson, C., Yang, Y., Rubin, B. E., Rifkin, S. A., Golden, J. W., & Golden, S. S.
- Affiliations
- University of California San Diego (US)
- Chinese Academy of Sciences (CN)
- Corresponding author
- Golden, Susan S.
- ORCID
- Venue
- Nature Communications
- Published
- 2020-04-03
- Volume
- 11
- Issue
- 1
- Pages
- 1688-1688
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC7125226
- OpenAlex
- W3014286189
- Cited by
- 110
- References
- 72
- Citations by year
- 2026: 18 · 2025: 17 · 2024: 13 · 2023: 16 · 2022: 21 · 2021: 14 · 2020: 11
- FWCI
- 7.96
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- Institute of Hydrobiology, CAS Institutional Repository (submittedVersion)
- Funders
- NSF | BIO | Division of Integrative Organismal Systems (IOS-1754894)
- U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R01GM118815, R35GM118290)
- Topics
- Life Sciences › Neuroscience › Endocrine and Autonomic Systems › Circadian rhythm and melatonin
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Light effects on plants
- Keywords
- circadian clock, natural competence, natural transformation, Anacystis nidulans, cyanobacteria, type IV pili, pilus biogenesis, darkness, dusk, day length, genome-wide screen, competence regulation
- MeSH terms
- Adaptation, Physiological, Bacterial Proteins, Darkness, DNA Transposable Elements, Models, Biological, Mutation, Fimbriae, Bacterial, Seasons, Transcription Factors, Transformation, Bacterial, Gene Expression Regulation, Bacterial, Gene Transfer, Horizontal, Synechococcus, Circadian Rhythm Signaling Peptides and Proteins, Circadian Clocks
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