New components of the community-based DNA-repair mechanism in Sulfolobales
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Abstract
After exposure to ultraviolet (UV) light, Sulfolobus acidocaldarius cells aggregate in a species-specific manner to exchange DNA and repair double-strand breaks via homologous recombination. The formation of cell–cell interactions is mediated by Ups pili. DNA exchange subsequently occurs through the Crenarchaeal system for exchange of DNA (Ced), which imports DNA. To identify novel players in these processes, we investigated that several genes upregulated after UV exposure, by creating in-frame deletion mutants and performing cell aggregation and DNA exchange assays. This led to the identification of two novel components involved in the Ups and Ced systems: UpsC, a minor pilin of the Ups pili, and CedD, a VirD4-like ATPase essential for DNA import. Altogether, these findings provide new insights into the DNA damage response mechanisms in Sulfolobales.
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Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
Fiji: an open-source platform for biological-image analysis
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2019 · Cited by 66,890 · see citing works
Huerta‐Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S. K., Cook, H., Mende, D. R., Letunić, I., Rattei, T., Jensen, L. J., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1085 · Cited by 4,943 · see citing works
Database resources of the national center for biotechnology information
Sayers, E. W., Bolton, E. E., Brister, J. R., Canese, K., Chan, J., Comeau, D. C., Connor, R., Funk, K., Kelly, C., Kim, S., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1112 · Cited by 2,812 · see citing works
Varadi, M., Bertoni, D., Magana, P., Paramval, U., Pidruchna, I., Radhakrishnan, M., Tsenkov, M., Nair, S., Mirdita, M., Yeo, J., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad1011 · Cited by 2,052 · cited 1× · see citing works
“For DNA exc hange, cells wer e gr own to an OD of 0.4–0.5, spun down at 75 ◦ C for 20 min at 3000 × g , and resus-pended in warm Br oc k media without uracil to a theoretical OD of 0.7.”
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Hallgren, J., Tsirigos, K. D., Pedersen, M. D., Armenteros, J. J. A., Marcatili, P., Nielsen, H., Krogh, A., & Winther, O. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.08.487609 · Cited by 1,528 · see citing works
Sulfolobus: A new genus of sulfur-oxidizing bacteria living at low pH and high temperature
Brock, T. D., Brock, K. M., Belly, R. T., & Weiss, R. L. (1972) · Archives of Microbiology · doi:10.1007/bf00408082 · Cited by 1,263 · see citing works
Prediction of glycosylation across the human proteome and the correlation to protein function
Gupta, R., & Brunak, S. (2001) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789812799623_0029 · Cited by 1,021 · see citing works
Induction of Competence Regulons as a General Response to Stress in Gram-Positive Bacteria
Claverys, J., Prudhomme, M., & Martin, B. (2006) · Annual Review of Microbiology · doi:10.1146/annurev.micro.60.080805.142139 · Cited by 415 · see citing works
The structural biology of type IV secretion systems
Fronzes, R., Christie, P. J., & Waksman, G. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2218 · Cited by 412 · see citing works
Iyer, L. M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh828 · Cited by 327 · see citing works
Versatile Genetic Tool Box for the Crenarchaeote Sulfolobus acidocaldarius
Wagner, M. M., van Wolferen, M., Wagner, A., Lassak, K., Meyer, B. H., Reimann, J., & Albers, S. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00214 · Cited by 212 · see citing works
Self-citationSyntTax: a web server linking synteny to prokaryotic taxonomy
Oberto, J. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-4 · Cited by 203 · see citing works
Szabó, Z., Stahl, A. O., Albers, S., Kissinger, J. C., Driessen, A. J. M., & Pohlschröder, M. (2006) · Journal of Bacteriology · doi:10.1128/jb.01547-06 · Cited by 170 · see citing works
Self-citationEfficient Prediction of Nucleic Acid Binding Function from Low-resolution Protein Structures
Szilágyi, A., & Skolnick, J. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.02.053 · Cited by 166 · see citing works
The Pacific Symposium on Biocomputing 2013
Turner, S. (2013) · doi:10.59350/trkr6-bgm87 · Cited by 160 · see citing works
Korotkov, K. V., & Hol, W. G. J. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1426 · Cited by 154 · see citing works
The Mosaic Type IV Secretion Systems
Christie, P. J. (2016) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0020-2015 · Cited by 149 · see citing works
Fröls, S., Ajon, M., Wagner, M. M., Teichmann, D., Zolghadr, B., Folea, M., Boekema, E. J., Driessen, A. J. M., Schleper, C., & Albers, S. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06459.x · Cited by 148 · see citing works
Self-citationStress-Induced Production of Biofilm in the Hyperthermophile Archaeoglobus fulgidus
Lapaglia, C., & Hartzell, P. L. (1997) · Applied and Environmental Microbiology · doi:10.1128/aem.63.8.3158-3163.1997 · Cited by 148 · see citing works
Jones, D., & Baxter, B. K. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01882 · Cited by 146 · see citing works
Response of the Hyperthermophilic Archaeon Sulfolobus solfataricus to UV Damage
Fröls, S., Gordon, P. M. K., Arcellana‐Panlilio, M. Y., Duggin, I. G., Bell, S. D., Sensen, C. W., & Schleper, C. (2007) · Journal of Bacteriology · doi:10.1128/jb.01016-07 · Cited by 129 · see citing works
Structural and functional diversity of type IV secretion systems
Costa, T. R. D., Patkowski, J. B., Macé, K., Christie, P. J., & Waksman, G. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00974-3 · Cited by 128 · see citing works
The essential genome of the crenarchaeal model Sulfolobus islandicus
Zhang, C., Phillips, A. P. R., Wipfler, R. L., Olsen, G. J., & Whitaker, R. J. (2018) · Nature Communications · doi:10.1038/s41467-018-07379-4 · Cited by 123 · see citing works
DNA Uptake by Type IV Filaments
Piepenbrink, K. H. (2019) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2019.00001 · Cited by 122 · see citing works
Hyperthermophiles and the problem of DNA instability
Grogan, D. W. (1998) · Molecular Microbiology · doi:10.1046/j.1365-2958.1998.00853.x · Cited by 120 · see citing works
UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili
Ajon, M., Fröls, S., van Wolferen, M., Stoecker, K., Teichmann, D., Driessen, A. J. M., Grogan, D. W., Albers, S., & Schleper, C. (2011) · Molecular Microbiology · doi:10.1111/j.1365-2958.2011.07861.x · Cited by 120 · see citing works
Self-citationResponses of hyperthermophilic crenarchaea to UV irradiation
Götz, D., Paytubi, S., Munro, S., Lundgren, M., Bernander, R., & White, M. F. (2007) · Genome biology · doi:10.1186/gb-2007-8-10-r220 · Cited by 118 · see citing works
Exchange of genetic markers at extremely high temperatures in the archaeon Sulfolobus acidocaldarius
Grogan, D. W. (1996) · Journal of Bacteriology · doi:10.1128/jb.178.11.3207-3211.1996 · Cited by 102 · see citing works
Structure and function of minor pilins of type IV pili
Jacobsen, T., Bardiaux, B., Francetić, O., Izadi‐Pruneyre, N., & Nilges, M. (2019) · Medical Microbiology and Immunology · doi:10.1007/s00430-019-00642-5 · Cited by 92 · see citing works
Protein secretion in the Archaea: multiple paths towards a unique cell surface
Albers, S., Szabó, Z., & Driessen, A. J. M. (2006) · Nature Reviews Microbiology · doi:10.1038/nrmicro1440 · Cited by 79 · see citing works
Self-citationDNA repair in the archaea—an emerging picture
White, M. F., & Allers, T. (2018) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuy020 · Cited by 78 · see citing works
The archaeal Ced system imports DNA
van Wolferen, M., Wagner, A., van der Does, C., & Albers, S. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1513740113 · Cited by 75 · see citing works
Self-citationHow hyperthermophiles adapt to change their lives: DNA exchange in extreme conditions
van Wolferen, M., Ajon, M., Driessen, A. J. M., & Albers, S. (2013) · Extremophiles · doi:10.1007/s00792-013-0552-6 · Cited by 57 · see citing works
Self-citationMolecular analysis of the UV‐inducible pili operon from Sulfolobus acidocaldarius
van Wolferen, M., Ajon, M., Driessen, A. J. M., & Albers, S. (2013) · MicrobiologyOpen · doi:10.1002/mbo3.128 · Cited by 46 · see citing works
Self-citationAllosteric activation of cell wall synthesis during bacterial growth
Shlosman, I., Fivenson, E. M., Gilman, M. S. A., Sisley, T. A., Walker, S., Bernhardt, T. G., Kruse, A. C., & Loparo, J. J. (2023) · Nature Communications · doi:10.1038/s41467-023-39037-9 · Cited by 45 · see citing works
van Wolferen, M., Shajahan, A., Heinrich, K., Brenzinger, S., Black, I. M., Wagner, A., Briegel, A., Azadi, P., & Albers, S. (2020) · mBio · doi:10.1128/mbio.03014-19 · Cited by 40 · see citing works
Self-citationA Variety of Bacterial Pili Involved in Horizontal Gene Transfer
Filloux, A. (2010) · Journal of Bacteriology · doi:10.1128/jb.00424-10 · Cited by 37 · see citing works
Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery
Beltrán, L. C., Cvirkaitė‐Krupovič, V., Miller, J., Wang, F., Kreutzberger, M. A. B., Patkowski, J. B., Costa, T. R. D., Stefan Schouten, A., Levental, I., Conticello, V. P., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36349-8 · Cited by 36 · see citing works
Chauhan, S., Poudel, S., Rychel, K., Lamoureux, C. R., Yoo, R., Bulushi, T. A., Yuan, Y., Palsson, B. Ø., & Sastry, A. V. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.753521 · Cited by 32 · see citing works
Feng, X., Sun, M., Han, W., Liang, Y. X., & She, Q. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky236 · Cited by 30 · see citing works
Meyer, B. H., Birich, A., & Albers, S. (2014) · Biochimie · doi:10.1016/j.biochi.2014.10.018 · Cited by 26 · see citing works
Self-citationSchult, F., Le, T. N., Albersmeier, A., Rauch, B., Blumenkamp, P., van der Does, C., Goesmann, A., Kalinowski, J., Albers, S., & Siebers, B. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky527 · Cited by 26 · see citing works
Self-citationGrogan, D. W., & Hansen, J. E. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.4.1266-1272.2003 · Cited by 21 · see citing works
CryoEM reveals the structure of an archaeal pilus involved in twitching motility
Gaines, M. C., Sivabalasarma, S., Isupov, M. N., Haque, R. U., McLaren, M., Hanus, C., Gold, V. A. M., Albers, S.-V., & Daum, B. (2024) · Nature Communications · doi:10.1038/s41467-024-45831-w · Cited by 20 · see citing works
Self-citationHuang, Q., Lin, Z., Wu, P., Ni, J., & Shen, Y. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.586025 · Cited by 18 · see citing works
Charles‐Orszag, A., van Wolferen, M., Lord, S. J., Albers, S., & Mullins, R. D. (2024) · Nature Communications · doi:10.1038/s41467-024-49101-7 · Cited by 17 · see citing works
Self-citationDissection of key determinants of cleavage activity in signal peptidase III (SPaseIII) PibD
Henche, A., van Wolferen, M., Ghosh, A., & Albers, S. (2014) · Extremophiles · doi:10.1007/s00792-014-0675-4 · Cited by 14 · see citing works
Self-citationSofer, S., Vershinin, Z., Mashni, L., Zalk, R., Shahar, A., Eichler, J., & Grossman‐Haham, I. (2024) · Nature Communications · doi:10.1038/s41467-024-50277-1 · Cited by 12 · see citing works
A conserved hexanucleotide motif is important in UV-inducible promoters in Sulfolobus acidocaldarius
Le, T. N., Wagner, A., & Albers, S. (2017) · Microbiology · doi:10.1099/mic.0.000455 · Cited by 8 · see citing works
Self-citationSuzuki, S., & Kurosawa, N. (2019) · Microbes and Environments · doi:10.1264/jsme2.me19055 · Cited by 7 · see citing works
Identification of novel components of the Ced and Ups systems in Saccharolobus islandicus REY15A
Wu, P., Zhang, M., Kou, Y., Liang, S., Ni, J., Huang, Q., & Shen, Y. (2025) · mLife · doi:10.1002/mlf2.12163 · Cited by 3 · see citing works
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Samson, R. Y., Takemata, N., & Bell, S. D. (2025) · Nature Communications · doi:10.1038/s41467-025-67934-8 · Cited by 3 · see citing works
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Wu, P., Gan, Q., Li, H., Liang, S., Yang, Y., Li, S., Xie, Y., Huang, Q., Feng, X., Yuan, G., et al. (2026) · Engineering Microbiology · doi:10.1016/j.engmic.2026.100262 · Cited by 2 · see citing works
Wu, P., Yang, Y., Gan, Q., Liang, S., Li, H., Li, S., Xie, Y., Huang, Q., Ni, J., & Shen, Y. (2026) · Springer eBooks · doi:10.1007/978-981-95-6970-0_7
- Authors
- Recalde, A., Wagner, A., Sivabalasarma, S., Yurmashava, A., Fehr, N. P., Thurm, R., Le, T. N., Köebler, C., Wassmer, B., Albers, S.-V., & van Wolferen, M.
- Affiliations
- University of Freiburg (DE)
- Molecular Biology of Archaea, Institute of Biology II—Microbiology, University of Freiburg , 79104 Freiburg ,
- Corresponding author
- Albers, Sonja-Verena
- ORCID
- Venue
- microLife
- Publisher
- Oxford University Press (OUP)
- Published
- 2025
- Volume
- 6
- Pages
- uqaf002-uqaf002
- ISSN
- 2633-6693 (ISSN-L)
- PMC
- PMC11823120
- OpenAlex
- W4406605637
- Cited by
- 3
- References
- 52
- Citations by year
- 2026: 2 · 2025: 1
- FWCI
- 0.90
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- microLife (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- FreiDok plus (Universitätsbibliothek Freiburg) (submittedVersion)
- Funders
- DFG (426849454, AL1206)
- University of Freiburg
- VW Momentum (94993)
- Deutsche Forschungsgemeinschaft
- Ministry of Education and Training (911)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Keywords
- Sulfolobales, DNA repair, homologous recombination, DNA double-strand break repair, cell aggregation, UV-induced DNA damage, DNA damage response, archaea
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