SPP 2330

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Publications

2023

  • Kohm K*, Jalomo Khayrova E*, Krüger A, Basu S, Steinchen W, Bange G, Frunzke J, Hertel R, Commichau FM, Czech L. Structural and functional characterization of MrpR, the master repressor of the Bacillus subtilis prophage SPβ, Nucleic Acids Research, 2023; gkad675, https://doi.org/10.1093/nar/gkad675
  • Wolfram-Schauerte M, Höfer K. NAD-capped RNAs – a redox cofactor meets RNA (2023) Trends in Biochemical Sciences, 48(2):142-155 DOI: 10.1016/j.tibs.2022.08.004
  • Rousset F, Sorek R. (2023) The evolutionary success of regulated cell death in bacterial immunity.  Current Opinion in Microbiology, 74:102312.
  • Hochhauser D, Millman A, Sorek R. (2023) The defense island repertoire of the Escherichia coli pan-genome. PLoS Genetics, 19(4):e1010694.
  • Stokar-Avihail A, Fedorenko T, Hör J, Garb J, Leavitt A, Millman A, Shulman G, Wojtania N, Melamed S, Amitai G, Sorek R. (2023) Discovery of phage determinants that confer sensitivity to bacterial immune systems. Cell, 186(9):1863-1876.e16.
  • Sun J, Ru J, Ramos-Mucci L, Qi F, Chen Z, Chen S, Cribbs AP, Deng L, Wang X. (2023) DeepsmirUD: Prediction of Regulatory Effects on microRNA Expression Mediated by Small Molecules Using Deep Learning. Int J Mol Sci. 18;24(3):1878. doi: 10.3390/ijms24031878. 
  • Luthe, T., Kever, L., Thormann, K., & Frunzke, J. (2023). Bacterial multicellular behavior in antiviral defense. Current opinion in microbiology, 74, 102314. Advance online publication. https://doi.org/10.1016/j.mib.2023.102314
  • Luthe, T., Kever, L., Hänsch, S., Hardy, A., Tschowri, N., Weidtkamp-Peters, S., & Frunzke, J. (2023). Streptomyces development is involved in the efficient containment of viral infections. microLife, 4, uqad002. https://doi.org/10.1093/femsml/uqad002
  • Hardy, A., Kever, L., & Frunzke, J. (2023). Antiphage small molecules produced by bacteria – beyond protein-mediated defenses. Trends in microbiology, 31(1), 92–106. https://doi.org/10.1016/j.tim.2022.08.001

2022

  • Leavitt, A., Yirmiya, E., Amitai, G., Lu, A., Garb, J., Herbst, E., Morehouse, B. R., Hobbs, S. J., Antine, S. P., Sun, Z. J., Kranzusch, P. J., & Sorek, R. (2022). Viruses inhibit TIR gcADPR signalling to overcome bacterial defence. Nature, 611(7935), 326–331. https://doi.org/10.1038/s41586-022-05375-9
  • Gehlert FO, Sauerwein T, Weidenbach K, Repnik U, Hallack D, Förstner KU, Schmitz RA. Dual-RNAseq Analysis Unravels Virus-Host Interactions of MetSV and Methanosarcina mazei. Viruses. 2022; 14(11):2585. https://doi.org/10.3390/v14112585
  • Kupczok A, Bailey ZM, Refardt D, Wendling CC. Co-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages. Microb Genom. 2022 Nov;8(11):mgen000915. doi: 10.1099/mgen.0.000915.
  • Garb, J., Lopatina, A., Bernheim, A., Zaremba, M., Siksnys, V., Melamed, S., Leavitt, A., Millman, A., Amitai, G., & Sorek, R. (2022). Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion. Nature microbiology, 7(11), 1849–1856. https://doi.org/10.1038/s41564-022-01207-8
  • Rohmer C, Dobritz R, Tuncbilek-Dere D, Lehmann E, Gerlach D, George SE, Bae T, Nieselt K, Wolz C.  Influence of Staphylococcus aureus Strain Background on Sa3int Phage Life Cycle Switches. Viruses. 2022 Nov 8;14(11):2471. doi: 10.3390/v14112471.
  • Hobbs SJ, Wein T, Lu A,  Morehouse BR, Schnabel J, Leavitt A, Yirmiya E, Sorek R & Kranzusch PJ. Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity (2022) Nature 605, 522–526  https://doi.org/10.1038/s41586-022-04716-y
  • Wolfram-Schauerte M, Pozhydaieva N, Viering M, Glatter T, Höfer K. (2022) Integrated Omics Reveal Time-Resolved Insights into T4 Phage Infection of E. coli on Proteome and Transcriptome Levels. Viruses. 12;14(11):2502. doi: 10.3390/v14112502

  • Tal N, Millman A, Stokar-Avihail A, Fedorenko T, Leavitt A, Melamed S, Yirmiya E, Avraham C, Brandis A, Mehlman T, Amitai G, Sorek R. Bacteria deplete deoxynucleotides to defend against bacteriophage infection (2022) Nature Microbiology, 7(8):1200-1209 (2022).

  • Venturini C, Petrovic Fabijan A, Fajardo Lubian A, Barbirz S, Iredell J. Biological foundations of successful bacteriophage therapy. EMBO Mol Med. 2022 Jul 7;14(7):e12435. doi: 10.15252/emmm.202012435.
  • Aguirre Sourrouille Z, Schwarzer S, Lequime S, Oksanen HM, Quax TEF. The Viral Susceptibility of the Haloferax Species. Viruses. 2022 Jun 20;14(6):1344. doi: 10.3390/v14061344.
  • Kever L, Hardy A, Luthe T, Hünnefeld M, Gätgens C, Milke L, Wiechert J, Wittmann J, Moraru C, Marienhagen J, Frunzke J. (2022) Aminoglycoside Antibiotics Inhibit Phage Infection by Blocking an Early Step of the Infection Cycle. mBio. 4:e0078322. doi: 10.1128/mbio.00783-22

2021

  • Weidenbach K, Wolf S, Kupczok A, Kern T, Fischer MA, Reetz J, Urbańska N, Künzel S, Schmitz RA, Rother M. Characterization of Blf4, an Archaeal Lytic Virus Targeting a Member of the Methanomicrobiales. Viruses. 2021 Sep 26;13(10):1934. doi: 10.3390/v13101934.
  • Tal N, Morehouse BR, Millman A, Stokar-Avihail A, Avraham C, Fedorenko T, Yirmiya E, Herbst E, Brandis A, Mehlman T, Oppenheimer-Shaanan Y, Keszei AFA, Shao S, Amitai G, Kranzusch PJ and Sorek R. (2021) Cyclic CMP and cyclic UMP mediate bacterial immunity against phages. Cell.184(23):5728-5739.e16. doi: 10.1016/j.cell.2021.09.031
  • Patens:

    Höfer K. (2021). RNAylation-tag – PCT application number: PCT/EP2021/071295.

Preliminary Results

  • Höfer K*, Schauerte M, Grawenhoff J, Wulf A, Welp LM, Billau FA, Urlaub H, Jäschke A* (2021) Viral ADP-ribosyltransferases attach RNA chains to host proteins. bioRxiv, doi: https://doi.org/10.1101/2021.06.04.446905
  • Schauerte M, Pozhydaieva N, Höfer K* (2021) Shaping the Bacterial Epitranscriptome—5′-Terminal and Internal RNA Modifications. Advanced Biology, doi: https://doi.org/10.1002/adbi.202100834
  • Tittes C, Schwarzer S, Pfeiffer F, Dyall-Smith M, Rodriguez-Franco M, Oksanen H.M., Quax T.E.F. *(2021) Cellular and genomic properties of Haloferax gibbonsii LR2-5, the host of euryarchaeal virus HFTV1. Frontiers in Microbiology, 16;12:625599.
  • Irmscher T, Roske Y, Gayk I, Dunsing V, Chiantia S, Heinemann U, Barbirz S (2021) Pantoea stewartii WceF is a glycan biofilm modifying enzyme with a bacteriophage tailspike-like fold, J. Biol. Chem. 296, 100286. https://doi:10.1016/j.jbc.2021.100286
  • Bange G, Brodersen DE, Liuzzi A and Steinchen W. (2021) Two P or Not Two P: Understanding Regulation by the Bacterial Second Messengers (p)ppGpp. Annu Rev Microbiol. 75:383-406. 10.1146/annurev-micro-042621-122343
  • Lamy-Besnier Q, Koszul R, Debarbieux L, Marbouty M. Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community. Microbiol Resour Announc. 2021 Apr 29;10(17):e01396-20. doi: 10.1128/MRA.01396-20.
  • Zhang, R., Mirdita, M., Levy Karin, E., Norroy, C., Galliez, C., and Söding, J. (2021) SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts. Bioinformatics, btab222. https://doi.org/10.1093/bioinformatics/btab222
  • Du X, Larsen J, Li M, Walter A, Slavetinsky C, Both A, Sanchez Carballo PM, Stegger M, Lehmann E, Liu Y, Liu J, Slavetinsky J, Duda KA, Krismer B, Heilbronner S, Weidenmaier C, Mayer C, Rohde H, Winstel V, Peschel A (2021) Staphylococcus epidermidis clones express Staphylococcus aureus-type wall teichoic acid to shift from a commensal to pathogen lifestyle. Nat Microbiol. 6:757-768.
  • Turzynski V, Monsees I, Moraru C, Probst AJ. (2021) Imaging techniques for detecting prokaryotic viruses in environmental samples. Viruses 13(11), 2126
  • Rohmer, C., and C. Wolz. 2021. The Role of hlb-Converting Bacteriophages in Staphylococcus aureus Host Adaption. Microb Physiol 31:109-122. https://www.ncbi.nlm.nih.gov/pubmed/34126612
  • Hardy A, Sharma V, Kever L, and Frunzke J (2020) Genome Sequence and Characterization of Five Bacteriophages Infecting Streptomyces Coelicolor and Streptomyces Venezuelae: Alderaan, Coruscant, Dagobah, Endor1 and Endor2. Viruses, doi: https://doi.org/10.3390/v12101065. 
  • Steinchen W, Zegarra V and Bange G (2020) (p)ppGpp: Magic Modulators of Bacterial Physiology and Metabolism. Front. Microbiol. 11:2072. doi: 10.3389/fmicb.2020.02072
  • Bernheim A, Sorek R (2020) The pan-immune system of bacteria: antiviral defence as a community resource. Nature Reviews Microbiology, 18(2):113-119.
  • Lourenço M, Chaffringeon L, Lamy-Besnier Q, Pédron T, Campagne P, Eberl C, Bérard M, Stecher B, Debarbieux L, De Sordi L. The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages. Cell Host Microbe. 2020 Sep 9;28(3):390-401.e5. doi: 10.1016/
  • Spriewald S, Stadler E, Hense BA, Münch PC, McHardy AC, Weiss AS, Obeng N, Müller J, Stecher B. Evolutionary Stabilization of Cooperative Toxin Production through a Bacterium-Plasmid-Phage Interplay. mBio. 2020 Jul 21;11(4):e00912-20. doi: 10.1128/mBio.00912-20.
  • E.L. Simmons, M.C. Bond, B. Koskella, K. Drescher, V. Bucci, C.D. Nadell (2020) Biofilm structure promotes coexistence of phage-resistant and phage-susceptible bacteria. mSphere 5, e00877-19.
  • Loessner, H., Schlattmeier, I., Anders-Maurer, M., Bekeredjian-Ding, I., Rohde, C., Wittmann, J., Pokalyuk, C., Krut, O.,Kamp, C. (2020) Kinetic Fingerprinting Links Bacteria-Phage Interactions with Emergent Dynamics: Rapid depletion of Klebsiella pneumoniae Indicates Phage Synergy Antibiotics 9(7), 408,  https://doi.org/10.3390/antibiotics9070408
  • Wenzel, S., M.M. Shneider, P.G. Leiman, A. Kuhn and D. Kiefer (2020). The central spike complex of bacteriophage T4 contacts PpiD in the periplasm of Escherichia coli. Viruses 12, 1135
  • Herber, J., Klotz, F., Frommeyer, B., Weis, S., Straile, D., Kolar, A., Sikorski, J., Egert, M., Dannenmann, M., Pester, M. (2020) A single Thaumarchaeon drives nitrification in deep oligotrophic Lake Constance. Environ Microbiol 22: 212-228
  • Duarte C.M., Ngugi D.K., Alam I., Pearman J., Kamau A., Eguilz V.W., Gojobori T., Acinas S.G., Gasol J.M., Bajic V.B., and Irigoien X. (2020) Sequencing effort dictates gene discovery in marine microbial metagenomes. Environ Microbiol. 22: 4589-4603
  • Rahlff J, Turzynski V, Esser SP, Monsees I, Bornemann TLV, Figueroa-Gonzalez PA, Schulz F, Woyke T, Klingl A, Moraru C, and Probst AJ (2020). Lytic archaeal viruses infect abundant primary producers in Earth’s crust. Nature Communications 12, 4642
  • Chibani CM, Mahnert A, Borrel G, Almeida A, Werner A, Brugère J-F, Gribaldo S, Finn RD, Schmitz RA, Moissl-Eichinger C (2020) A comprehensive analysis of the global human gut archaeome from a thousand genome catalogue. bioRxiv 2020.11.21.392621; doi: 10.1101/2020.11.21.392621
  • Borrel G, Brugère JF, Gribaldo S, Schmitz RA, Moissl-Eichinger C (2020) The host-associated archaeome. Nature Reviews Microbiology, 1-15, DOI: 10.1038/s41579-020-0407-y
  • Gerovac M, Wicke L, Chihara K, Schneider C, Lavigne R, Vogel J (2020) A Grad-seq view of RNA and protein complexes in Pseudomonas aeruginosa under standard and bacteriophage predation conditions. mBio 12(1):e03454-20, doi: https://doi.org/10.1128/mBio.03454-20.
  • Wicke L, Ponath F, Coppens L, Gerovac M, Lavigne R, Vogel J (2020) Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage ɸKZ. RNA Biology 18(8):1099-1110, doi: 10.1080/15476286.2020.1827785.
  • Dunsing V, Irmscher T, Barbirz S, Chiantia S (2019) Purely Polysaccharide-Based Biofilm Matrix Provides Size-Selective Diffusion Barriers for Nanoparticles and Bacteriophages. Biomacromolecules, 20, 3842-3854. https://doi:10.1021/acs.biomac.9b00938
  • Peschek N, Hoyos M, Herzog R, Förstner KU, Papenfort K (2019) A conserved seed-pairing domain affords small RNA-mediated stress resistance in enterobacteria. The EMBO Journal, 15;38(16).
  • Yoon, G., Gaynanova, I., & Müller, C. L. (2019). Microbial networks in SPRING – Semi-parametric rank-based correlation and partial correlation estimation for quantitative microbiome data,” Front. Genet., vol. 10, 1–28.
  • Zborowsky, S. and D. Lindell. (2019) Resistance in marine cyanobacteria differs against specialist and generalist cyanophages. Proc. Nat. Acad. Sci. USA. 116:16899-16908, www.pnas.org/cgi/doi/10.1073/pnas.1906897116.
  • Kupczok A, Dagan T. 2019. Rates of Molecular Evolution in a Marine Synechococcus Phage Lineage. Viruses 11:720.
  • Bischoff, V., Bunk, B., Meier-Kolthoff, J.P., Spröer, C., Poehlein, A., Dogs, M., Nguyen, M., Petersen, J., Daniel, R., Overmann, J., Göker, M., Simon, M., Brinkhoff T. and Moraru, C. (2019) Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. The ISME Journal 13 (6), pp. 1404-1421.
  • Reimer LC, Vetcininova A, Sardà Carbasse J, Söhngen C, Gleim D, Ebeling C, Overmann J (2019) BacDive in 2019: Bacterial phenotypic data for high-throughput biodiversity analysis. Nucl Acids Res 47(D1):D631-D636.
  • Korf IHE, Meier-Kolthoff JP, Adriaenssens EM, Kropinski AM, Nimtz M, Rohde M, van Raaij MJ, Wittmann J (2019) Still Something to Discover: Novel Insights into Escherichia coli Phage Diversity and Taxonomy. Viruses 11(5):454.
  • Ingmer, H., D. Gerlach, and C. Wolz. 2019. Temperate Phages of Staphylococcus aureus. Microbiol Spectr 7. https://www.ncbi.nlm.nih.gov/pubmed/31562736
  • Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R (2018) Systematic discovery of antiphage defense systems in the microbial pangenome. Science, 359(6379), pii: eaar4120.
  • Vidakovic, P.K. Singh, R. Hartmann, C.D. Nadell, K. Drescher (2018) Dynamic biofilm architecture confers individual and collective mechanisms of viral protection. Nature Microbiology 3, 26-3.
  • Kupczok A, Neve H, Huang KD, Hoeppner MP, Heller KJ, Franz CMAP, Dagan T. (2018) Rates of mutation and recombination in Siphoviridae phage genome evolution over three decades. Mol Biol Evol 35:1147–1159.
  • Gerlach D, Guo Y, De Castro C, Kim SH, Schlatterer K, Xu FF, Pereira C, Seeberger PH, Ali S, Codee J, Sirisan W, Schulte B, Wolz C, Larsen J, Molinaro A, Lee BL, Xia G, Stehle T, Peschel A (2018) Methicillin-resistant Staphylococcus aureus alters cell wall glycosylation to evade immunity. Nature 563:705-709
  • Matthew C Waller, Josef R Bober, Nikhil U Nair, Chase L Beisel (2017) Toward a genetic tool development pipeline for host-associated bacteria. Current Opinion in Microbiology, doi: https://doi.org/10.1016/j.mib.2017.05.006
  • Erdmann, S., Tschitschko, B., Zhong, L., Raftery M. & Cavicchioli R. A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells. Nat. Microbiol. 2:1446-1455 (2017).
  • Weidenbach K, Nickel L, Neve H, Alkhnbashi OS, Künzel S, Krupczok A, Bauersachs T, Tholey A, Schmitz RA (2017) MSV, a novel archaeal lytic virus targeting Methanosarcina strains. Journal of Virology 2017 Sep 6. 91(22). pii: e00955-17. doi: 10.1128/JVI.00955-17.
  • Steinchen W and Bange G (2016) The magic dance of the alarmones (p)ppGpp. Molecular Microbiology, 101: 531-544. https://doi.org/10.1111/mmi.13412
  • Brugiroux S., Beutler M., Pfann C., Garzetti D., Ruscheweyh H.J., Ring D., Diehl M., Herp S., Lötscher Y., Hussain S., Bunk B., Pukall R., Huson D.H., Münch P.C., McHardy A.C., McCoy K.D., Macpherson A.J., Loy A., Clavel T., Berry D., Stecher B. Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium. Nat Microbiol. 2016 Nov 21;2:16215. doi: 10.1038/nmicrobiol.2016.215. PMID: 27869789.
  • Ledermann, B., Beja, O. & Frankenberg-Dinkel, N. (2016) New biosynthetic pathway for pink pigments from uncultured oceanic viruses. Environ. Microbiol. 18, 4337-4347
  • Lorenz, N., Reiger, M., Toro-Nahuelpan, M. Brachmann, A., Poettinger, L., Plener, L., Lassak, J., Jung, K. (2016) Identification and initial characterization of prophages in Vibrio campbellii, PLoS One, 11: e0156010.
  • Nedialkova L.P., Sidstedt M., Koeppel M.B., Spriewald S., Ring D., Gerlach R.G., Bossi L. and Stecher B. Temperate phages promote colicin-dependent fitness of Salmonella enterica serovar Typhimurium. Environmental Microbiology. 2015 Oct 6. doi: 10.1111/1462-2920.13077.
  • *Doron S., *Fedida A., Hernández-Prieto M.A., Sabehi G., Karunker I., Stazic D., Feingersch R., Steglich C., Futschik M., #Lindell D. and #Sorek R. (2015) Transcriptome dynamics of a broad host-range cyanophage and its hosts. ISME J 10, https://doi.org/10.1038/ismej.2015.210. *contributed equally, #corresponding authors
  • Lupo, D., S. Leptihn, G. Nagler, M. Haase, I. Molineux and A. Kuhn (2015). The T7 ejection nanomachine components gp15/gp16 form a spiral ring complex that binds DNA and a lipid membrane. Virology 486, 263-271.
  • Deng L, Ignacio-Espinoza JS, Gregory A, Poulos PT, Weitz JS, Hugenholtz P, Sullivan MB. (2014) Viral tagging reveals discrete populations in Synechococcus viral genome sequence space, Nature 513, 242-245.