PSOSP uncovers pervasive SOS-independent prophages with distinct genomic and host traits in bacterial genomes

Yali Hao , Mujie Zhang , Xinjuan Lei , Chengrui Zhu , Taoliang Zhang , Yanping Zheng , Xiang Xiao , Huahua Jian

iMeta ›› 2025, Vol. 4 ›› Issue (5) : e70073

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iMeta ›› 2025, Vol. 4 ›› Issue (5) :e70073 DOI: 10.1002/imt2.70073
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PSOSP uncovers pervasive SOS-independent prophages with distinct genomic and host traits in bacterial genomes
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Yali Hao, Mujie Zhang, Xinjuan Lei, Chengrui Zhu, Taoliang Zhang, Yanping Zheng, Xiang Xiao, Huahua Jian. PSOSP uncovers pervasive SOS-independent prophages with distinct genomic and host traits in bacterial genomes. iMeta, 2025, 4(5): e70073 DOI:10.1002/imt2.70073

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References

[1]

Silveira, Cynthia B., Antoni Luque, and Forest Rohwer. 2021. “The Landscape of Lysogeny Across Microbial Community Density, Diversity and Energetics.” Environmental Microbiology 23: 4098-4111. https://doi.org/10.1111/1462-2920.15640

[2]

Howard-Varona, Cristina, Katherine R. Hargreaves, Stephen T. Abedon, and Matthew B. Sullivan. 2017. “Lysogeny in Nature: Mechanisms, Impact and Ecology of Temperate Phages.” The ISME Journal 11: 1511-1520. https://doi.org/10.1038/ismej.2017.16

[3]

Feiner, Ron, Tal Argov, Lev Rabinovich, Nadejda Sigal, Ilya Borovok, and Anat A. Herskovits. 2015. “A New Perspective on Lysogeny: Prophages as Active Regulatory Switches of Bacteria.” Nature Reviews Microbiology 13: 641-650. https://doi.org/10.1038/nrmicro3527

[4]

Erill, Ivan, Susana Campoy, and Jordi Barbé. 2007. “Aeons of Distress: An Evolutionary Perspective on the Bacterial SOS Response.” FEMS Microbiology Reviews 31: 637-656. https://doi.org/10.1111/j.1574-6976.2007.00082.x

[5]

Butala, M., D. Žgur-Bertok, and S. J. W. Busby. 2009. “The Bacterial LexA Transcriptional Repressor.” Cellular and Molecular Life Sciences 66: 82-93. https://doi.org/10.1007/s00018-008-8378-6

[6]

Zhang, Adrianna P. P., Ying Z. Pigli, and Phoebe A. Rice. 2010. “Structure of the LexA-DNA Complex and Implications for SOS Box Measurement.” Nature 466: 883-886. https://doi.org/10.1038/nature09200

[7]

Nickels, Bryce E. 2009. “A New Twist on a Classic Paradigm: Illumination of a Genetic Switch in Vibrio cholerae Phage CTXФ.” Journal of Bacteriology 191: 6779-6781. https://doi.org/10.1128/jb.01150-09

[8]

Brady, Aisling, Alonso Felipe-Ruiz, Francisca Gallego del Sol, Alberto Marina, Nuria Quiles-Puchalt, and José R. Penadés. 2021. “Molecular Basis of Lysis-Lysogeny Decisions in Gram-Positive Phages.” Annual Review of Microbiology 75: 563-581. https://doi.org/10.1146/annurev-micro-033121-020757

[9]

Oppenheim, Amos B., Oren Kobiler, Joel Stavans, Donald L. Court, and Sankar Adhya. 2005. “Switches in Bacteriophage Lambda Development.” Annual Review of Genetics 39: 409-429. https://doi.org/10.1146/annurev.genet.39.073003.113656

[10]

Knowles, Ben, Barbara Bailey, Lance Boling, Mya Breitbart, Ana Cobián-Güemes, Javier del Campo, Rob Edwards, et al. 2017. “Variability and Host Density Independence in Inductions-Based Estimates of Environmental Lysogeny.” Nature Microbiology 2: 17064. https://doi.org/10.1038/nmicrobiol.2017.64

[11]

Mahmoud, Aminu Abdullahi, Xiaoyu Wang, Xinyu Liao, Song Zhang, Tian Ding, and Juhee Ahn. 2025. “Impact of Prophages on Gut Microbiota and Disease Associations.” Microbial Pathogenesis 204: 107642. https://doi.org/10.1016/j.micpath.2025.107642

[12]

Wong, Joel W. H., and Emily P. Balskus. 2025. “Small Molecules as Modulators of Phage-Bacteria Interactions.” Current Opinion in Chemical Biology 84: 102566. https://doi.org/10.1016/j.cbpa.2024.102566

[13]

Fernández de Henestrosa, Antonio R., Tomoo Ogi, Sayura Aoyagi, David Chafin, Jeffrey J. Hayes, Haruo Ohmori, and Roger Woodgate. 2000. “Identification of Additional Genes Belonging to the LexA Regulon in Escherichia coli.” Molecular Microbiology 35: 1560-1572. https://doi.org/10.1046/j.1365-2958.2000.01826.x

[14]

Kelley, William L. 2006. “Lex Marks the Spot: The Virulent Side of SOS and a Closer Look at the LexA Regulon.” Molecular Microbiology 62: 1228-1238. https://doi.org/10.1111/j.1365-2958.2006.05444.x

[15]

Erill, Ivan, Mónica Jara, Noelia Salvador, Marcos Escribano, Susana Campoy, and Jordi Barbé. 2004. “Differences in LexA Regulon Structure Among Proteobacteria through In Vivo Assisted Comparative Genomics.” Nucleic Acids Research 32: 6617-6626. https://doi.org/10.1093/nar/gkh996

[16]

Erill, Ivan, Marcos Escribano, Susana Campoy, and Jordi Barbé. 2003. “In Silico Analysis Reveals Substantial Variability in the Gene Contents of the Gamma Proteobacteria LexA-Regulon.” Bioinformatics 19: 2225-2236. https://doi.org/10.1093/bioinformatics/btg303

[17]

Lewis, L. Kevin, Greg R. Harlow, Leslie A. Gregg-Jolly, and David W. Mount. 1994. “Identification of High Affinity Binding Sites for LexA Which Define New DNA Damage-Inducible Genes in Escherichia coli.” Journal of Molecular Biology 241: 507-523. https://doi.org/10.1006/jmbi.1994.1528

[18]

Jian, Huahua, Lei Xiong, Guanpeng Xu, and Xiang Xiao. 2016. “Filamentous Phage SW1 Is Active and Influences the Transcriptome of the Host at High-Pressure and Low-Temperature.” Environmental Microbiology Reports 8: 358-362. https://doi.org/10.1111/1758-2229.12388

[19]

Haft, Daniel H., Azat Badretdin, George Coulouris, Michael DiCuccio, A Scott Durkin, Eric Jovenitti, Wenjun Li, et al. 2024. “RefSeq and the Prokaryotic Genome Annotation Pipeline in the Age of Metagenomes.” Nucleic Acids Research 52: D762-D769. https://doi.org/10.1093/nar/gkad988

[20]

Sayers, Eric W., Mark Cavanaugh, Karen Clark, Kim D. Pruitt, Conrad L. Schoch, Stephen T. Sherry, and Ilene Karsch-Mizrachi. 2021. “GenBank.” Nucleic Acids Research 49: D92-D96. https://doi.org/10.1093/nar/gkaa1023

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