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Department of Pharmacy and Biotechnology - FABIT

Molecular Biology and Genomics of Prokaryotes. Coordinator: Roncarati

Study of the molecular mechanisms underlying the regulation of bacterial virulence, with particular emphasis on protein transcriptional regulators and non-coding RNAs, using integrated approaches in molecular biology, -omics methodologies, and bioinformatics.

Areas: Genomics

The research group focuses on the study of gene regulation in major bacterial pathogens, with particular attention to bacterial pathogenesis, mechanisms of response to environmental stimuli and stress conditions, and the molecular processes governing host–pathogen interactions. The group’s research activity is centered on the role of protein regulators, particularly transcriptional regulators, and non-coding RNAs in transcriptional and post-transcriptional regulatory processes controlling bacterial virulence and adaptive responses.

The main research lines include:

  • Investigation of transcriptional regulatory mechanisms involved in bacterial responses to a wide range of environmental stimuli, such as heat shock, oxidative stress, and metal ion availability. This research relies on genome-wide approaches (RNA sequencing and ChIP sequencing) integrated with molecular and structural methods to define regulatory mechanisms and regulator–DNA interactions.
  • Functional characterization of bacterial non-coding RNAs and the molecular mechanisms underlying their regulatory activity, through the integration of -omics approaches and molecular biology techniques.

Lab Members

Davide Roncarati, Associate Professor

Andrea Vannini, Associate Professor

Clelia Manna, PhD student

Mattia Nicolò Li Volsi, PhD student

Internship projects

  • One or two positions per year for students enrolled in Master’s degree programs.
  • Two or three positions per year for students enrolled in Bachelor’s degree programs

The internship activities for selected students will be directly related to the research projects of the group, as described above.

Main publications

  • D'Agostino F, Pinatel E, Meynhardt A, Scarlato V, Vannini A, Roncarati D. (2025). RNase Y mediates posttranscriptional control of the virulence-associated CncR1 small-RNA in Helicobacter pylori. iScience. 28(2):111815.https://doi.org/10.1016/j.isci.2025.111815
  • Vannini A, Pinatel E, Costantini PE, Pelliciari S, Roncarati D, Puccio S, De Bellis G, Scarlato V, Peano C, Danielli A. (2024). (Re)-definition of the holo- and apo-Fur direct regulons of Helicobacter pylori. J Mol Biol. 436(10):168573.https://doi.org/10.1016/j.jmb.2024.168573
  • Antoniciello F, Roncarati D, Zannoni A, Chiti E, Scarlato V. & Chiappori F. (2022). Targeting the Essential Transcription Factor HP1043 of Helicobacter pylori: A Drug Repositioning Study. Frontiers in molecular biosciences, 2022, 9: 887564. https://doi.org/10.3389/fmolb.2022.887564
  • Roncarati D, Pelliciari S, Doniselli N, Maggi S, Vannini A, Valzania L, Mazzei L, Zambelli B, Rivetti C, Danielli A. (2016). Metal-responsive promoter DNA compaction by the ferric uptake regulator. Nat Commun. 7:12593. https://doi.org/10.1038/ncomms12593
  • Vannini A, Roncarati D, Danielli A. (2016). The cag-pathogenicity island encoded CncR1 sRNA oppositely modulates Helicobacter pylori motility and adhesion to host cells. Cell Mol Life Sci. 73(16):3151-68. https://doi.org/10.1007/s00018-016-2151-z

Contacts