Publications

by SPP2020 members and associates

2021

  • Melior H, Li S, Stötzel M, Maaß S, Schütz R, Azarderakhsh S, Shevkoplias A, Barth-Weber S, Baumgardt K, Ziebuhr J, Förstner KU, Chervontseva Z, Becher D, Evguenieva-Hackenberg E. Reprograming of sRNA target specificity by the leader peptide peTrpL in response to antibiotic exposure. Nucleic Acids Res. 2021 Mar 18;49(5):2894-2915. doi: 10.1093/nar/gkab093. PMID: 33619526; PMCID: PMC7968998.

 

  • Melior H, Evguenieva-Hackenberg E. RNA-Regulation und Antibiotikaresistenz: Trans-agierende Attenuator-RNA und Leaderpeptid in Bakterien. Biospektrum 2021; 02.21:127-130. doi:10.1007/s12268­021­1545­0

 

  • Gutt M, Jordan B, Weidenbach K, Gudzuhn M, Kiessling C, Cassidy L, Helbig A, Tholey A, Pyper DJ, Kubatova N, Schwalbe H, Schmitz RA. High complexity of Glutamine synthetase regulation in Methanosarcina mazei: Small protein 26 interacts and enhances glutamine synthetase activity. FEBS J. 2021 Mar 4. doi: 10.1111/febs.15799. Epub ahead of print. PMID: 33660383.

 

  • Krauspe V, Fahrner M, Spät P, Steglich C, Frankenberg-Dinkel N, Maček B, Schilling O, Hess WR. Discovery of a small protein factor involved in the coordinated degradation of phycobilisomes in cyanobacteria. Proc Natl Acad Sci USA. Feb 2021. 2;118(5):e2012277118. doi: 10.1073/pnas.2012277118. PMID: 33509926.

 

2020

  • Wylensek D, Hitch TCA, Riedel T, Afrizal A, Kumar N, Wortmann E, Liu T, Devendran S, Lesker TR, Hernández SB, Heine V, Buhl EM, M D’Agostino P, Cumbo F, Fischöder T, Wyschkon M, Looft T, Parreira VR, Abt B, Doden HL, Ly L, Alves JMP, Reichlin M, Flisikowski K, Suarez LN, Neumann AP, Suen G, de Wouters T, Rohn S, Lagkouvardos I, Allen-Vercoe E, Spröer C, Bunk B, Taverne-Thiele AJ, Giesbers M, Wells JM, Neuhaus K, Schnieke A, Cava F, Segata N, Elling L, Strowig T, Ridlon JM, Gulder TAM, Overmann J, Clavel T. A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. Nat Commun. 2020 Dec 15;11(1):6389. doi: 10.1038/s41467-020-19929-w. PMID: 33319778; PMCID: PMC7738495.

 

  • Kubatova N, Jonker HRA, Saxena K, Richter C, Vogel V, Schreiber S, Marchfelder A* and Schwalbe H*. Solution structure and dynamics of the small protein HVO_2922 from Haloferax volcanii. Chembiochem. Jan 2020; 21(1-2):149‐156; doi:10.1002/cbic.201900085                                     

        * joint corresponding author

 

  • Schuller JM, Saura P, Thiemann J, Schuller SK, Gamiz-Hernandez AP, Kurisu G, Nowaczyk MM, Kaila VRI Redox-Coupled Proton Pumping Drives Carbon Concentration in the Photosynthetic Complex I.
    Nat Commun. 2020;11(1):494. Jan 2020; doi: 10.1038/s41467-020-14347-4

 

  • Petruschke H, Anders J, Stadler PF, Jehmlich N, von Bergen M. Enrichment and identification of small proteins in a simplified human gut microbiome. J Proteomics. Feb 2020;213:103604; doi: 10.1016/j.jprot.2019.103604

 

  • Bernheim A, Sorek R. The pan-immune system of bacteria: antiviral defence as a community resource. Nat Rev Microbiol Feb 2020,  2020;18(2):113‐119. doi:10.1038/s41579-019-0278-2

 

  • Kubatova N, Pyper D, Jonker HRA, Saxena K, Remmel L, Richter C, Brantl S, Evguenieva-Hackenberg E, Hess WR, Klug G, Marchfelder A, Soppa J, Streit W, Mayzel M, Orekhov VY, Fuxreiter M, Schmitz RA, Schwalbe H. Rapid biophysical characterization and NMR structural analysis of small proteins from bacteria and archaea. Chembiochem. Apr 2020; 21(8):1178‐1187. doi: 10.1002/cbic.201900677

 

  • Krause JL, Schaepe SS, Fritz-Wallace K, Engelmann B, Rolle-Kampczyk U, Kleinsteuber S, Schattenberg F, Liu Z, Mueller S, Jehmlich N, von Bergen M., Herberth G. Following the community development of SIHUMIx – a new intestinal in vitro model for bioreactor use. Jul 2020, Gut Microbes. 2020;1‐14. doi:10.1080/19490976.2019.1702431

 

  • Gutt M, Jordan B, Weidenbach K, Gudzuhn M, Kiessling C, Cassidy L, Helbig A, Tholey A, Pyper D, Schwalbe H, Schmitz RA. Small protein 26 interacts and enhances glutamine synthetase activity in Methanosarcina mazei. bioRxiv (2020), doi: 10.1101/2020.05.06.080432.

 

  • Bartholomäus A, Kolte B, Mustafayeva A, Goebel I, Fuchs S, Engelmann S, Ignatova Z. smORFer: a modular algorithm to detect small ORFs in prokaryotes. bioRxiv (2020); doi: 10.1101/2020.05.21.109181.

 

  • Knoke LR, Abad Herrera S, Götz K, Justesen BH, Günther Pomorski T, Fritz C, Schäkermann S, Bandow JE and Aktas M. Agrobacterium tumefaciens small lipoprotein Atu8019 is involved in selective outer membrane vesicle (OMV) docking to bacterial cells. Front. Microbiol. June 2020,11:1228. doi: 10.3389/fmicb.2020.01228

 

  • Fuchs S, Kucklick M, Lehmann E, Beckmann A, Wilkens M, Kolte B, Mustafayeva A, Ludwig T, Diwo M, Wissing J, Jänsch L, Ahrens CH, Ignatova Z, Engelmann S A proteogenomics workflow to uncover the world of small proteins in Staphylococcus aureus. bioRxiv. 2020, doi: 10.1101/2020.05.25.114132

 

  • Yadavalli SS*, Carey JN, Malengo G, Vellappan S, Nickels BE, Sourjik V, Goulian M* and Yuan J*. Functional determinants of a small protein controlling a broadly conserved bacterial sensor kinase. J. Bacterol. June 2020, DOI: 10.1128/JB.00305-20          *corresponding authors
    • highlighted in the Spotlight section of Journal of  Bacteriology

 

  • Melior H, Maaß S, Li S, Förstner KU, Azarderakhsh S, Varadarajan AR, Stötzel M, Elhossary M, Barth-Weber S, Ahrens CH, Becher D, Evguenieva-Hackenberg E. The leader peptide peTrpL forms antibiotic-containing ribonucleoprotein complexes for posttranscriptional regulation of multiresistance genes. mBio. June 2020, doi: 10.1128/mBio.01027-20.

 

  • Bartholomäus A, Ignatova Z. Codon Resolution Analysis of Ribosome Profiling Data. Methods Mol Biol. 2021;2252:251-268. doi: 10.1007/978-1-0716-1150-0_12. PMID: 33765280.

 

  • Zahn S, Kubatova N, Pyper DJ, Cassidy L, Saxena K, Tholey A, Schwalbe H, Soppa J. Biological functions, genetic and biochemical characterization, and NMR structure determination of the small zinc finger protein HVO_2753 from Haloferax volcanii. FEBS J. 2021 Mar;288(6):2042-2062. doi: 10.1111/febs.15559. Epub 2020 Sep 24. PMID: 32905660.

 

  • Schulze S, Adams Z, Cerletti M, De Castro R, Ferreira-Cerca S, Inés Giménez M, Hippler M, Jevtic Z, Knüppel R, Legerme G, Lenz C, Marchfelder A, Maupin-Furlow JA, Paggi RA, Pfeiffer F, Poetsch A, Urlaub H and Pohlschroder M. The Archaeal Proteome Project – advancing knowledge about archaeal cell biology through comprehensive proteomics. Nature Communications June 2020, in press; DOI: 10.1038/s41467-020-16784-7

 

  • de Alvarenga L V , Hess W R and Hagemann M. AcnSP – A Novel Small Protein Regulator of Aconitase Activity in the Cyanobacterium Synechocystis sp. PCC 6803. Frontiers in Microbiology June 2020. https://doi.org/10.3389/fmicb.2020.01445

 

 

  • Venturini E, Svensson SL, Maaß S, Gelhausen R, Eggenhofer F, Li L, Cain AK, Parkhil J, Becher D, Backofen R, Barquist L, Sharma CM, Westermann AJ, Vogel J. A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence. bioRxiv 2020, 05.26.116038; doi: 10.1101/2020.05.26.116038

 

  • Gelhausen R, Heyl F, Svensson SL, Froschauer K, Hadjeras L, Sharma CM, Eggenhofer F, Backofen R. HRIBO – High-throughput analysis of bacterial ribosome profiling data. bioRxiv 2020, 04.27.046219; doi: 10.1101/2020.04.27.046219

 

  • Kraus A, Weskamp M, Zierles J, Balzer M, Busch R, Eisfeld E, Lambertz J, Nowaczyk MM,  Narberhaus F. Arginine-rich small proteins with a domain of unknown function DUF1127 play a role in phosphate and carbon metabolism of Agrobacterium tumefaciens. J Bacteriol 2020. doi: 10.1128/JB.00309-20

 

    • Published comment: Alakavuklar M A and Fuqua C. Short, Rich, and Powerful: A New Family of Arginine-Rich Small Proteins Have Outsized Impact in Agrobacterium tumefaciens. J Bacteriol Aug. 2020. doi:10.1128/JB.00450-20

 

  • Bartholomäus A, Kolte B, Mustafayeva A, Goebel I, Fuchs S, Engelmann S, Ignatova Z. smORFer: a modular algorithm to detect small ORFs in prokaryotes. biorXiv 2020. Under peer-review.

 

  • Ul Haq I, Müller P and Brantl S. SR7 – a dual-function antisense RNA from Bacillus subtilis. RNA Biol 2020. doi: 10.1080/15476286.2020.1798110

 

  • Kaulich P T, Cassidy L, Weidenbach K, Schmitz R A, Tholey A. Complementarity of Different SDS-PAGE Gel Staining Methods for the Identification of Short Open Reading Frame-encoded Peptides. Proteomics July 2020. In press. https://doi.org/10.1002/pmic.202000084

 

  • Bartel J, Varadarajan A R, Sura T, Ahrens C H, Maaß S, Becher D. An Optimised Proteomics Workflow for the Detection of Small Proteins. Journal of Proteome Research Aug 2020. https://doi.org/10.1021/acs.jproteome.0c00286

 

  • Voichek M, Maaß S, Kroniger T, Becher D, Sorek R. Peptide-based quorum sensing systems in Paenibacillus polymyxa. Life Science Alliance Aug. 2020. DOI: 10.26508/lsa.202000847

 

  • Steenhuis M , Koningstein G M, Oswald J, Pick T, O’Keefe S, Koch HG, Cavalié A, Whitehead R C, Swanton E, High S, Luirink J. Eeyarestatin 24 Impairs SecYEG-dependent Protein Trafficking and Inhibits Growth of Clinically Relevant Pathogens. Molecular Microbioloy Aug 2020. In press. DOI: 10.1111/mmi.14589

 

  • Steinberg R, Origi A, Natriashvili A, Sarmah P, Licheva M, Walker PM, Kraft C, High S, Luirink J, Shi WQ, Helmstädter M, Ulbrich MH, Koch HG. Posttranslational insertion of small membrane proteins by the bacterial signal recognition particle. PLoS Biol. 2020 Sep 30;18(9):e3000874. doi: 10.1371/journal.pbio.3000874. PMID: 32997663; PMCID: PMC7549839.

 

  • Zahn S, Kubatova N, Pyper DJ, Cassidy L, Saxena K, Tholey A, Schwalbe H, Soppa J. Biological functions, genetic and biochemical characterization, and NMR structure determination of the small zinc finger protein HVO_2753 from Haloferax volcanii. FEBS Sept 2020. DOI: 10.1111/febs.15559

 

  • Cassidy L, Helbig AO, Kaulich PT, Weidenbach K, Schmitz RA & Tholey A. Multidimensional separation schemes enhance the identification and molecular characterization of low molecular weight proteomes and short open reading frame encoded peptides in top-down proteomics. J Proteomics Sept 2020, in press

 

  • Edelmann D, Oberpaul M, Schäberle TF, Berghoff BA. Post-transcriptional deregulation of the tisB/istR-1 toxin-antitoxin system promotes SOS-independent persister formation in Escherichia coli. Environ Microbiol Rep. Dec 2020. doi: 10.1111/1758-2229.12919.
 

2019

  • Ben-Zvi T, Pushkarev A, Seri H, Elgrably-Weiss M, Papenfort K, Altuvia S. mRNA dynamics and alternative conformations adopted under low and high arginine concentrations control polyamine biosynthesis in Salmonella. PLoS Genet. 2019;15(2):e1007646. Feb 2019. doi: 10.1371/journal.pgen.1007646

 

  • Voichek M, Maaß S, Kroniger T, Becher D, Sorek R. Peptide-based quorum sensing systems in Paenibacillus polymyxa. Biorxiv (2019) doi: 10.1101/767517

 

  • Stokar-Avihail A, Tal N, Erez Z, Lopatina A, Sorek R. Widespread Utilization of Peptide Communication in Phages Infecting Soil and Pathogenic Bacteria. Cell Host Microbe. 2019;25(5):746‐755.e5. doi: 10.1016/j.chom.2019.03.017

 

  • Edelmann D, Berghoff BA. Type I toxin-dependent generation of superoxide affects the persister life cycle of Escherichia coli. Sci Rep. 2019;9(1):14256. Oct 2019. doi: 10.1038/s41598-019-50668-1

 

  • Schape SS, Krause JL, Engelmann B, Fritz-Wallace K, Schattenberg F, Liu Z, Muller S, Jehmlich N, Rolle-Kampczyk U, Herberth G, von Bergen M. The Simplified Human Intestinal Microbiota (SIHUMIx) Shows High Structural and Functional Resistance against Changing Transit Times in In Vitro Bioreactors. Microorganisms. 2019;7(12):641. Dec 2019. doi: 10.3390/microorganisms7120641

 

  • Jevtic Z, Stoll B, Pfeiffer F, Sharma K, Urlaub, H, Marchfelder A*, Lenz, C* The response of Haloferax volcanii to salt and temperature stress: a proteome study by label-free mass spectrometry. Proteomics 2019, 2019;19(20):e1800491. doi: 10.1002/pmic.201800491                                    * joint corresponding author

 

  • Stachler AE, Schwarz TS, Schreiber S, Marchfelder A. CRISPRi as an efficient tool for gene repression in Archaea. Methods pii: S1046-2023(18)30472-9. doi: 10.1016/j.ymeth.2019.05.023.

 

  • Schuller JM, Birrell JA, Tanaka H, Konuma T, Wulfhorst H, Cox N, Schuller SK, Thiemann J, Lubitz W, Sétif P, Ikegami T, Engel BD, Kurisu G, Nowaczyk MM. Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer. Science. 2019;363(6424):257‐260. doi: 10.1126/science.aau3613

 

  • Knüpffer L, Fehrenbach C, Denks K, Erichsen V, Petriman NA, Koch HG. Molecular mimicry of SecA and signal recognition particle binding to the bacterial ribosome. mBio Aug 2019. 2019;10(4):e01317-19. doi: 10.1128/mBio.01317-19

 

  • Utz M, Andrei A, Milanov M, Trasnea PI, Marckmann D, Daldal F, Koch HG. The Cu chaperone CopZ is required for Cu homeostasis in Rhodobacter capsulatus and influences cytochrome cbb3 oxidase assembly. Mol Microbiol. 2019;111(3):764‐783. doi:10.1111/mmi.14190

 

  • Origi A, Natriashvili A, Knüpffer L, Fehrenbach C, Denks K, Asti R, Koch HG. Yet another role for the bacterial ribosome. Microb Cell Oct 2019. 2019;6(11):524‐526. doi: 10.15698/mic2019.11.698

 

  • Berghoff BA, Wagner EGH. (2019) Persister Formation Driven by TisB-Dependent Membrane Depolarization. In: Lewis K. (eds) Persister Cells and Infectious Disease. Springer International Publishing, Cham. pp. 77–97.

 

  • Nagel C, Machulla A, Zahn S, Soppa J. Several One-Domain Zinc Finger µ-Proteins of Haloferax Volcanii Are Important for Stress Adaptation, Biofilm Formation, and Swarming. Genes (Basel) May 2019. 2019;10(5):361. doi: 10.3390/genes10050361

 

  • Cassidy L, Kaulich PT, Tholey A. Depletion of High-Molecular-Mass Proteins for the Identification of Small Proteins and Short Open Reading Frame Encoded Peptides in Cellular Proteomes. J Proteome Res 2019. 2019;18(4):1725‐1734. doi: 10.1021/acs.jproteome.8b00948

 

2018

  • Ofir G, Sorek R. Contemporary Phage Biology: From Classic Models to New Insights. Cell. 2018;172(6):1260‐1270. doi: 10.1016/j.cell.2017.10.045

 

  • Steinberg R, Knüpffer L, Origi A, Asti R, Koch HG. Co-translational protein targeting in bacteria. FEMS Microbiol Lett. 2018;365(11):10.1093/femsle/fny095. doi:10.1093/femsle/fny095

 

2017

  • Denks K, Sliwinski N, Erichsen V, Borodkina B, Origi A, Koch HG. The signal recognition particle contacts uL23 and scans substrate translation inside the ribosomal tunnel. Nat Microbiol. 2017;2:16265. Published 2017 Jan 30. doi:10.1038/nmicrobiol.2016.265

 

  • Yuan J, Jin F, Glatter T, Sourjik V. Osmosensing by the bacterial PhoQ/PhoP two-component system. PNAS Dec 2017. DOI: 10.1073/pnas.1717272114