Junior Research Group Bacterial RNA Biology

Bacterial small RNAs (sRNAs) act as key elements in regulatory networks to control gene expression at the post-transcriptional level. Most sRNAs function through direct base-pairing interactions with target transcripts, leading to changes in stability, processing and translation of the recognized mRNA. Their abilities to act on multiple transcripts and to exert both positive and negative regulation make sRNAs highly versatile and valuable molecules to help bacteria adapt to changing environmental conditions. While hundreds of sRNA candidates have been identified in genome-wide bioinformatic-based or experimental screens in enterobacteria, the bulk of studies investigating the function and mechanisms of sRNAs have been focusing on Escherichia coli or its close relatives. In our group, we use Caulobacter crescentus and Klebsiella pneumoniae as model organisms to study the principles of RNA-mediated processes in bacteria, and to uncover novel mechanisms of bacterial gene regulation.

• Costafrolaz J, Degeorges L, Panis G, Vallet SU, Velasco Gomariz M, Meireles FTP, Dal Peraro M, Fröhlich KS, Viollier PH (2026) Asymmetric envelope surface disposition of secreted protein YjbI controls bimodal antibiotic susceptibilities in C. crescentus. EMBO J 45(3):987-1023
• Vogt LN, Gomariz MV, Siemers M, Papenfort K, Fröhlich KS (2025) An RNA sponge directs the transition from feast to famine in Caulobacter crescentus. Nat Commun 16(1):9478
• Velasco-Gomariz M, Sulzer J, Faber F and Fröhlich KS (2025) An sRNA overexpression library reveals AbnZ as a negative regulator of an essential translocation module in Caulobacter crescentus. Nucleic Acids Res 53, gkae1139
• Bandyra KJ, Fröhlich KS, Vogel J, Rodnina M, Goyal A and Luisi BF (2024) Cooperation of regulatory RNA and the RNA degradosome in transcript surveillance. Nucleic Acids Res 52, 9161-9173
• Vogt LN, Panis G, Schäpers A, Peschek N, Huber M, Papenfort K, Viollier PH and Fröhlich KS (2024) Genome-wide profiling of Hfq-bound RNAs reveals the iron-responsive small RNA RusT in Caulobacter crescentus. mBio, 15, e0315323
• Ruhland E, Siemers M, Gerst R, Späth F, Vogt LN, Figge MT, Papenfort K and Fröhlich KS (2024) The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division. Proc Natl Acad Sci U S A, 121, e2317322121
• Peschek N, Herzog R, Singh PK, Sprenger M, Meyer F, Fröhlich KS, Schröger L, Bramkamp M, Drescher K and Papenfort K (2020) RNA-mediated control of cell shape modulates antibiotic resistance in Vibrio cholerae. Nat Commun, 11, 6067
• Huber M, Fröhlich KS, Radmer J and Papenfort K (2020) Switching fatty acid metabolism by an RNA-controlled feed forward loop. Proc Natl Acad Sci U S A, 117, 8044-8054
• Santiago-Frangos A, Fröhlich KS, Jeliazkov JR, Malecka EM, Marino G, Gray JJ, Luisi BF, Woodson SA and Hardwick SW (2019) Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation. Proc Natl Acad Sci U S A, 116, 10978-10987
• Herzog R, Peschek N, Fröhlich KS, Schumacher K and Papenfort K (2019) Three autoinducer molecules act in concert to control virulence gene expression in Vibrio cholerae. Nucleic Acids Res, 47, 3171-3183
• Chuang SK, Vrla GD, Fröhlich KS and Gitai Z (2019) Surface association sensitizes Pseudomonas aeruginosa to quorum sensing. Nat Commun, 10, 4118
• Bianco CM, Fröhlich KS, Vanderpool CK (2019) Bacterial Cyclopropane Fatty Acid Synthase mRNA is targeted by activating and repressing small RNAs. J Bacteriol 201(19)
• Santiago-Frangos A*, Fröhlich KS*, Jeliazkov JR, Małecka-Grajek EM, Marino G, Gray JJ, Luisi BF, Woodson SA, Hardwick SW (2019) Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation. Proc Nat Acad Sci 116(22):10978-10987
  *equally contributing authors
• Herzog R, Peschek N, Fröhlich KS, Schumacher K, Papenfort K (2019) Three autoinducer molecules act in concert to control virulence gene expression in Vibrio cholerae. Nucleic Acids Res 47(6):3171-3183 
• Fröhlich KS, Förstner KU, Gitai Z (2018) Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus. Nucleic Acids Res 46(20):10969-10982
• Fröhlich KS, Haneke K, Papenfort K, Vogel J (2016) The target spectrum of SdsR small RNA in Salmonella. Nucleic Acids Res 44(21): 10406-10422 
• Dimastrogiovanni D, Fröhlich KS, Bandyra KJ, Bruce HA, Hohensee S, Vogel J, Luisi BF (2014) Recognition of the small regulatory RNA RydC by the bacterial Hfq protein. Elife 2014 Dec 31;3
• Fröhlich KS, Papenfort K, Fekete A, Vogel J (2013) A small RNA activates CFA synthase by isoform-specific mRNA stabilization. Embo J 32(22):2963-79
• Fröhlich KS, Papenfort K, Berger AA, Vogel J (2012) A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD. Nucleic Acids Res 40(8): 3623-3640

• Fröhlich KS, and Velasco Gomariz M (2021) RNA-controlled regulation in Caulobacter crescentus. Curr Opin Microbiol 60: 1-7
• Fröhlich KS, and Papenfort K (2020) Regulation outside the box: New mechanisms for small RNAs. Mol Microbiol 114: 363-366
• Fröhlich KS, Gottesman S (2018) Small Regulatory RNAs in the Enterobacterial Response to Envelope Damage and Oxidative Stress. Microbiol Spectr 2018 Jul;6(4)
• Fröhlich KS, Papenfort K (2016) Interplay of regulatory RNAs and mobile genetic elements in enteric pathogens. Mol Microbiol 101(5):701-13
• Fröhlich KS, Vogel J (2009) Activation of gene expression by small RNA. Curr Opin Microbiol 12(6): 674-682

Manuel Velasco Gomariz

Maria Thamm (MSc. Microbiology)

Felix Späth (MSc. Microbiology)

Pia Müller (BSc. Biologie)

Maria Schreiber (BSc. Bioinformatik)