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Jun Prof Neva Caliskan

Recoding Mechanisms in Infections

Our research and approach

The research group lead by Neva Caliskan investigates functions and dynamics of RNA molecules in non-canonical translation events, which can affect the interplay between the host and pathogen during infection. Ultimately, they seek to illuminate therapeutic RNA-protein complexes as novel targets to combat infections.

Viruses and cellular genes encode RNAs that can be read in alternative ways during translation, which is called recoding. However, how exactly recoding is regulated by host encoded factors remains elusive. Here, a detailed understanding of recoding and its regulation can open doors for the development of novel RNA-based therapeutic interventions to combat infections.

Neva Caliskan’s group investigates the functions and dynamics of RNA molecules and their interplay with trans-acting factors involved in recoding events. They work with several viruses known to depend on recoding strategies for replication including corona and retroviruses, and develop methods to investigate RNA complexes and translation in unprecedented detail.

The group employs a highly interdisciplinary toolset including RNA-antisense purification and mass spectrometry to identify RNA-interaction partners, and cellular assays to investigate molecular details. Ensemble and single molecule assays such as optical tweezers are key to study the dynamics of RNA complexes. Ultimately, they seek to understand how RNA-structure elements act in concert with other factors in the cell to modulate the way mRNA messages are read by ribosomes during infections to advance RNA-based therapeutics.

Team members

Anuja Kibe

Anuja Kibe

PhD Student

Lukáš Pekárek

Lukáš Pekárek

PhD Student

Ricarda Riegger

Ricarda Riegger

PhD Student

Tatyana Koch

Tatyana Koch

Technical Assistant

Stefan Buck

Stefan Buck

Data Manager

Research projects

Many bacterial and viral pathogens and also their eukaryotic host cells employ non-canonical translation strategies in order to express hidden genes from alternative open reading frames (Caliskan et al., 2015). RNA is a versatile molecule that acts as a key regulator of non-canonical translation events. RNA can exist in various shapes and interact with other regulatory elements such as ncRNAs, small molecules and proteins to alter the meaning of the message encoded in the primary sequence of the mRNA. How RNA structure and regulatory elements drive alternative translation events is currently not fully understood. In addition, it is largely unclear to what extend these translation events are used by the pathogen and the host cell during infections. We use cutting-edge RNA analytics, such as ribosome profiling and deep sequencing combined with single molecule and computational tools to understand dynamics of translation and the functions of RNA regulators during infections. Ultimately, we want to better understand the interplay between the host’s and pathogen’s gene expression and harness our knowledge to develop novel therapeutic strategies to combat infectious diseases.

The POTATO TOOL: DATA ANALYSIS MAde easy

The single-molecule technique known as optical tweezers allows probing of intra- and intermolecular interactions that govern complex biological processes. Recent developments have made it easier to collect data, yet it remains difficult to analyze it. To enable high-throughput data analysis, we developed an automated Python-based analysis pipeline called POTATO (practical optical tweezers analysis tool). POTATO uses predefined parameters to automatically process the high-frequency raw data generated by force-ramp experiments and to identify (un)folding events. Our research was published in the Biophysical Journal.

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Publications

2022

Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging

Ye L, Gribling-Burrer AS, Bohn P, Kibe A, Börtlein C, Ambi UB, Ahmad S, Olguin-Nava M, Smith M, Caliskan N, von Kleist M, Smyth RP (2022)

Nature Structural & Molecular Biology 29 (4): 306-319

Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA

Liao C, Sharma S, Svensson SL, Kibe A, Weinberg Z, Alkhnbashi OS, Bischler T, Backofen R, Caliskan N, Sharma CM, Beisel CL (2022)

Nature Microbiology 7 (4): 530-541

Editorial: mRNA Translational Control as a Mechanism of Post-transcriptional Gene Regulation

Kiss DL, Vasudevan D, Ho CK, Caliskan N (2022)

Frontiers in Molecular Biosciences 9: 947516

POTATO: Automated pipeline for batch analysis of optical tweezers data

Buck S, Pekarek L, Caliskan N (2022)

Biophysical Journal 121 (15): 2830-2839

Insights from structural studies of the cardiovirus 2A protein

Caliskan N, Hill CH (2022)

Bioscience Reports 42 (1): 2021040

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Pekarek L, Buck S, Caliskan N (2022)

Journal of Visualized Experiments (180)

Thinking Outside the Frame: Impacting Genomes Capacity by Programmed Ribosomal Frameshifting

Riegger RJ, Caliskan N (2022)

Frontiers in Molecular Biosciences 9: 842261

2021

Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch

Hill CH, Pekarek L, Napthine S, Kibe A, Firth AE, Graham SC, Caliskan N, Brierley I (2021)

Nature Communications 12 (1): 7166

Investigating molecular mechanisms of 2A-stimulated ribosomal pausing and frameshifting in Theilovirus

Hill CH, Cook GM, Napthine S, Kibe A, Brown K, Caliskan N, Firth AE, Graham SC, Brierley I (2021)

Nucleic Acids Research 49 (20): 11938-11958

The short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting

Zimmer MM, Kibe A, Rand U, Pekarek L, Ye L, Buck S, Smyth RP, Cicin-Sain L, Caliskan N (2021)

Nature Communications 12 (1): 7193

2020

The SARS-CoV-2 RNA-protein interactome in infected human cells

Schmidt N, Lareau CA, Keshishian H, Ganskih S, Schneider C, Hennig T, Melanson R, Werner S, Wei Y, Zimmer M, …, Bodem J, Munschauer M (2020)

Nature Microbiology 6 (3): 339-353

2019

Thermodynamic control of -1 programmed ribosomal frameshifting

Bock LV, Caliskan N, Korniy N, Peske F, Rodnina MV, Grubmüller H (2019)

Nature Communications 10: 4598

2018

Small synthetic molecule-stabilized RNA pseudoknot as an activator for -1 ribosomal frameshifting

Matsumoto S, Caliskan N, Rodnina MV, Murata A, Nakatani K (2018)

Nucleic Acids Research 46 (16): 8079-8089

2017

Conditional Switch between Frameshifting Regimes upon Translation of dnaX mRNA

Caliskan N, Wohlgemuth I, Korniy N, Pearson M, Peske F, Rodnina MV (2017)

Molecular Cell 66 (4): 558-567

2016

Choreography of molecular movements during ribosome progression along mRNA

Belardinelli R, Sharma H, Caliskan N, Cunha CE, Peske F, Wintermeyer W, Rodnina MV (2016)

Nature Structural & Molecular Biology 23 (4): 342-8

2015

Changed in translation: mRNA recoding by -1 programmed ribosomal frameshifting

Caliskan N, Peske F, Rodnina MV (2015)

Trends in Biochemical Sciences 40 (5): 265-74

2014

Programmed -1 frameshifting by kinetic partitioning during impeded translocation

Caliskan N, Katunin VI, Belardinelli R, Peske F, Rodnina MV (2014)

Cell 157 (7): 1619-31