Anssi Malinen
Ph.D.
ansmal@utu.fi +358 29 450 4784 Tykistökatu 6 Turku Office: 6128 ORCID identifier: https://orcid.org/0000-0003-2987-2649 |
Areas of expertise
Biochemistry; enzyme and protein chemistry; enzyme kinetics, enzyme inhibitors molecular biology; mechanism of transcription; ion transporting membrane-bound pyrophosphatases; single molecule biophysics; university teacher
Biochemistry; enzyme and protein chemistry; enzyme kinetics, enzyme inhibitors molecular biology; mechanism of transcription; ion transporting membrane-bound pyrophosphatases; single molecule biophysics; university teacher
Biography
University lecturer 9/2022-
Academy research fellow, group leader 9/2017-8/2022 (5-year term).
Research topic: Regulation of eukaryotic transcription.
Researcher/University teacher at the University of Turku, Department of Biochemistry. 2016-2017.
Research topics: Mechanism of transcription & Molecular evolution of membrane-bound pyrophosphatases.
Postdoctoral fellow at the University of Oxford, Department of Physics. 2014-2016.
Research topic: Single molecule biophysics of bacterial transcription initiation.
Postdoctoral fellow at the University of Turku, Department of Biochemistry. 2009-2014.
Research topics: Mechanism of transcription elongation in bacteria & Mechanism of membrane-bound pyrophosphatases.
Doctoral candidate at the University of Turku, Department of Biochemistry. 2002-2009.
Research topic: Structure and function of membrane-bound pyrophosphatases.
Research
I am interested in the molecular function and regulatory mechanisms of transcription in eukaryotic species. Current projects in my research group revolve around RNA polymerase I (Pol I) that produces ribosomal RNA – building blocks of cell’s protein factories, ribosomes. The synthesis of ribosomal RNA by Pol I accounts for >60% of total transcription in growing eukaryotic cells and constitutes the rate-limiting step of ribosome biogenesis. Oversupply of ribosomes tightly links with accelerated cellular proliferation, while shortage induces cell cycle arrest, senescence or apoptosis in different cell types. To balance the capacity and demand of protein synthesis, many signaling networks that control cell cycle regulate Pol I. Importantly, dysregulation of Pol I activity is linked to the etiology of many human cancers and hereditary disorders.
To understand on the molecular level how the function of RNA polymerase I is regulated in normal and sick cells, we aim to elucidate the identity and sequence of molecular events that take place at the beginning of Pol I mediated production of ribosomal RNA. Our research approach depends on sophisticated biochemical, enzyme kinetic and single-molecule biophysics tools that we develop to monitor the function of Pol I in real-time. The molecular mechanisms that we will uncover pave the way for the development of new drugs that specifically constrain the function of Pol I and hence potentially slow down the progress of cancer and other diseases.
I am interested in the molecular function and regulatory mechanisms of transcription in eukaryotic species. Current projects in my research group revolve around RNA polymerase I (Pol I) that produces ribosomal RNA – building blocks of cell’s protein factories, ribosomes. The synthesis of ribosomal RNA by Pol I accounts for >60% of total transcription in growing eukaryotic cells and constitutes the rate-limiting step of ribosome biogenesis. Oversupply of ribosomes tightly links with accelerated cellular proliferation, while shortage induces cell cycle arrest, senescence or apoptosis in different cell types. To balance the capacity and demand of protein synthesis, many signaling networks that control cell cycle regulate Pol I. Importantly, dysregulation of Pol I activity is linked to the etiology of many human cancers and hereditary disorders.
To understand on the molecular level how the function of RNA polymerase I is regulated in normal and sick cells, we aim to elucidate the identity and sequence of molecular events that take place at the beginning of Pol I mediated production of ribosomal RNA. Our research approach depends on sophisticated biochemical, enzyme kinetic and single-molecule biophysics tools that we develop to monitor the function of Pol I in real-time. The molecular mechanisms that we will uncover pave the way for the development of new drugs that specifically constrain the function of Pol I and hence potentially slow down the progress of cancer and other diseases.
Teaching
Teaching interests:
Bioprocess technology, mammalian cell factories, enzyme and protein chemistry, transcription, gene regulation, membrane biology.
Publications 
1 of 2
- Aflatoxin biosynthesis regulators AflR and AflS : DNA binding affinity, stoichiometry, and kinetics (2024)
- Biochemical Journal
(A1 Refereed original research article in a scientific journal) - Functional and structural asymmetry suggest a unifying principle for catalysis in membrane-bound pyrophosphatases (2024)
- EMBO Reports
(A1 Refereed original research article in a scientific journal) - A methanolic extract of Zanthoxylum bungeanum modulates secondary metabolism regulator genes in Aspergillus flavus and shuts down aflatoxin production (2022)
- Scientific Reports
(A1 Refereed original research article in a scientific journal) - Pre-steady-state kinetics and solvent isotope effects support the "billiard-type" transport mechanism in Na+-translocating pyrophosphatase (2022)
- Protein Science
(A1 Refereed original research article in a scientific journal) - Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter (2022)
- Nucleic Acids Research
(A1 Refereed original research article in a scientific journal) - Real-Time Single-Molecule Studies of RNA Polymerase–Promoter Open Complex Formation Reveal Substantial Heterogeneity Along the Promoter-Opening Pathway (2022)
- Journal of Molecular Biology
(A1 Refereed original research article in a scientific journal) - The Mechanism of Energy Coupling in H+/Na+-Pumping Membrane Pyrophosphatase-Possibilities and Probabilities (2022)
- International Journal of Molecular Sciences
(A2 Refereed review article in a scientific journal ) - Catalytic asymmetry in homodimeric h+‐pumping membrane pyrophosphatase demonstrated by non‐hydrolyzable pyrophosphate analogs (2021)
- International Journal of Molecular Sciences
(A1 Refereed original research article in a scientific journal) - Good-Practice Non-Radioactive Assays of Inorganic Pyrophosphatase Activities (2021)
- Molecules
(A2 Refereed review article in a scientific journal ) - A Single-Molecule View on Cellular and Viral RNA Synthesis (2019) Biophysics of RNA-Protein Interactions: A Mechanistic View Ostrofet Eugen, Stal Papini Flavia, Malinen Anssi M, Dulin David
(A3 Refereed book chapter or chapter in a compilation book) - Oxazinomycin arrests RNA polymerase at the polythymidine sequences (2019)
- Nucleic Acids Research
(A1 Refereed original research article in a scientific journal) - Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria (2018)
- Nature Communications
(A1 Refereed original research article in a scientific journal) - Role of the potassium/lysine cationic center in catalysis and functional asymmetry in membrane-bound pyrophosphatases (2018)
- Biochemical Journal
(A1 Refereed original research article in a scientific journal) - Two independent evolutionary routes to Na+/H+ cotransport function in membrane pyrophosphatases. (2016)
- Biochemical Journal
(A1 Refereed original research article in a scientific journal) - Cytochrome cbb3 of Thioalkalivibrio is a Na+-pumping cytochrome oxidase (2015)
- Proceedings of the National Academy of Sciences of the United States of America
(A1 Refereed original research article in a scientific journal) - Evolutionarily divergent, Na+-regulated H+-transporting membrane-bound pyrophosphatases (2015)
- Biochemical Journal
(A1 Refereed original research article in a scientific journal) - Monitoring translocation of multisubunit RNA polymerase along the DNA with fluorescent base analogues (2015) Bacterial Transcriptional Control Malinen Anssi M., Turtola Matti, Belogurov Georgiy A.
(A3 Refereed book chapter or chapter in a compilation book) - CBR antimicrobials alter coupling between the bridge helix and the β subunit in RNA polymerase (2014)
- Nature Communications
(A1 Refereed original research article in a scientific journal) - Membrane-integral pyrophosphatase subfamily capable of translocating both Na+ and H+ (2013)
- Proceedings of the National Academy of Sciences of the United States of America
(A1 Refereed original research article in a scientific journal) - Membrane Na+-pyrophosphatases Can Transport Protons at Low Sodium Concentrations (2013)
- Journal of Biological Chemistry
(A1 Refereed original research article in a scientific journal)
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