I am a biochemist and neurobiologist interested in understanding the role of protein and membrane trafficking in synaptic plasticity and neurodegenerative diseases like Alzheimer's and Parkinson's disease.
Can supervise: YES
1. Protein and membrane traffiking in neurons.
2. Cellular and molecular mechanisms of Alzheimer's disease.
3. Neuroinflammation and cell signaling pathways.
4. Synaptic plasticity.
5. Protein biochemistry.
Bera, S, Camblor-Perujo, S, Calleja Barca, E, Negrete-Hurtado, A, Racho, J, De Bruyckere, E, Wittich, C, Ellrich, N, Martins, S, Adjaye, J & Kononenko, NL 2020, 'AP-2 reduces amyloidogenesis by promoting BACE1 trafficking and degradation in neurons', EMBO Reports, vol. 21, no. 6.View/Download from: Publisher's site
© 2020 The Authors. Published under the terms of the CC BY 4.0 license Cleavage of amyloid precursor protein (APP) by BACE-1 (β-site APP cleaving enzyme 1) is the rate-limiting step in amyloid-β (Aβ) production and a neuropathological hallmark of Alzheimer's disease (AD). Despite decades of research, mechanisms of amyloidogenic APP processing remain highly controversial. Here, we show that in neurons, APP processing and Aβ production are controlled by the protein complex-2 (AP-2), an endocytic adaptor known to be required for APP endocytosis. Now, we find that AP-2 prevents amyloidogenesis by additionally functioning downstream of BACE1 endocytosis, regulating BACE1 endosomal trafficking and its delivery to lysosomes. AP-2 is decreased in iPSC-derived neurons from patients with late-onset AD, while conditional AP-2 knockout (KO) mice exhibit increased Aβ production, resulting from accumulation of BACE1 within late endosomes and autophagosomes. Deletion of BACE1 decreases amyloidogenesis and mitigates synapse loss in neurons lacking AP-2. Taken together, these data suggest a mechanism for BACE1 intracellular trafficking and degradation via an endocytosis-independent function of AP-2 and reveal a novel role for endocytic proteins in AD.
Negrete-Hurtado, A, Overhoff, M, Bera, S, De Bruyckere, E, Schätzmüller, K, Kye, MJ, Qin, C, Lammers, M, Kondylis, V, Neundorf, I & Kononenko, NL 2020, 'Autophagy lipidation machinery regulates axonal microtubule dynamics but is dispensable for survival of mammalian neurons', Nature Communications, vol. 11, no. 1.View/Download from: Publisher's site
Sanchez-Mendoza, EH, Camblor-Perujo, S, Martins Nascentes-Melo, L, Dzyubenko, E, Fleischer, M, Silva de Carvalho, T, Schmitt, L-I, Leo, M, Hagenacker, T, Herring, A, Keyvani, K, Bera, S, Kononenko, N, Kleinschnitz, C & Hermann, DM 2020, 'Compromised Hippocampal Neuroplasticity in the Interferon-α and Toll-like Receptor-3 Activation-Induced Mouse Depression Model', Molecular Neurobiology, vol. 57, no. 7, pp. 3171-3182.View/Download from: Publisher's site
Kononenko, NL, Claßen, GA, Kuijpers, M, Puchkov, D, Maritzen, T, Tempes, A, Malik, AR, Skalecka, A, Bera, S, Jaworski, J & Haucke, V 2017, 'Retrograde transport of TrkB-containing autophagosomes via the adaptor AP-2 mediates neuronal complexity and prevents neurodegeneration', Nature Communications, vol. 8, no. 1.View/Download from: Publisher's site
Bera, S, Raghuram, V, Mikhaylova, M & Kreutz, MR 2016, 'A plasmid-based expression system to study protein-protein interactions at the Golgi in vivo', Analytical Biochemistry, vol. 502, pp. 50-52.View/Download from: Publisher's site
© 2016 Elsevier Inc. All rights reserved. There is still an unmet need for simple methods to verify, visualize, and confirm protein-protein interactions in vivo. Here we describe a plasmid-based system to study such interactions. The system is based on the transmembrane domain (TMD) of the EF-hand Ca2+ sensor protein calneuron-2. We show that fusion of 28 amino acids that include the TMD of calneuron-2 to proteins of interest results in prominent localization on the cytoplasmic side of the Golgi. The recruitment of binding partners to the protein of interest fused to this sequence can then be easily visualized by fluorescent tags.
Mikhaylova, M, Bera, S, Kobler, O, Frischknecht, R & Kreutz, MR 2016, 'A Dendritic Golgi Satellite between ERGIC and Retromer', Cell Reports, vol. 14, no. 2, pp. 189-199.View/Download from: Publisher's site
© 2016 The Authors. The local synthesis of transmembrane proteins underlies functional specialization of dendritic microdomains in neuronal plasticity. It is unclear whether these proteins have access to the complete machinery of the secretory pathway following local synthesis. In this study, we describe a probe called pGolt that allows visualization of Golgi-related organelles for live imaging in neurons. We show that pGolt labels a widespread microsecretory Golgi satellite (GS) system that is, in contrast to Golgi outposts, present throughout basal and apical dendrites of all pyramidal neurons. The GS system contains glycosylation machinery and is localized between ERGIC and retromer. Synaptic activity restrains lateral movement of ERGIC, GS, and retromer close to one another, allowing confined processing of secretory cargo. Several synaptic transmembrane proteins pass through and recycle back to the GS system. Thus, the presence of an ER-ERGIC-GS-retromer microsecretory system in all neuronal dendrites enables autonomous local control of transmembrane protein synthesis and processing. It is unclear whether post-endoplasmatic reticulum carriers in dendrites require a Golgi-related compartment for glycosylation or whether they bypass the Golgi. Mikhaylova et al. find a widespread ER-ERGIC-Golgi satellite-retromer microsecretory system in all dendrites of pyramidal neurons through which a spectrum of synaptic transmembrane proteins might pass and even recycle.
Bera, S, Thillai, K, Sriraman, K & Jayaraman, G 2015, 'Process strategies for enhancing recombinant streptokinase production in Lactococcus lactis cultures using P170 expression system', Biochemical Engineering Journal, vol. 93, pp. 94-101.View/Download from: Publisher's site
© 2014 Elsevier B.V. The production of recombinant proteins in Lactococcus lactis is often limited by several process and biological constraints. Recombinant gene expression in the P170 system of L. lactis is triggered at a pH below 6.5 by lactic acid accumulation. This work has used static flask, batch bioreactor and chemostat studies to independently investigate various factors affecting production of recombinant streptokinase. These factors are induction strength, complex-nutrient supplementation, specific growth rate and the cellular response to acid-stress termed as acid tolerance response (ATR). In the P170 system, induction strength is mainly a function of lactate concentration. Recombinant protein production is enhanced by increasing induction strength and complex-nutrient supplementation. However, acid-induced cellular stress-response has a deleterious effect on recombinant protein productivity. It is seen that suppression of ATR has the most predominant effect on enhancing recombinant protein productivity. The insights obtained from batch studies were used to investigate fed-batch processes, both during complete development of ATR and during suppression of ATR. During complete ATR-development, a 25-fold enhancement of volumetric productivity was achieved in fed-batch culture, due to a synergistic combination of increased glucose-feed rates and addition of complex-nutrients to the feed. A combination of these factors and ATR-suppression gave rise to nearly 60-fold increase in volumetric productivity in fed-batch culture over batch processes.
Bera, S & Kreutz, MR 2014, 'When synaptic proteins meet the genome: Transcriptional regulation in cell death and plasticity by the synapto-nuclear messenger jacob', Neuropsychopharmacology, vol. 39, no. 1, pp. 245-246.View/Download from: Publisher's site
Yuanxiang, P, Bera, S, Karpova, A, Kreutz, MR & Mikhaylova, M 2014, 'Isolation of CA1 nuclear enriched fractions from hippocampal slices to study activity-dependent nuclear import of synapto-nuclear messenger proteins', Journal of Visualized Experiments, no. 90.View/Download from: Publisher's site
Studying activity dependent protein expression, subcellular translocation, or phosphorylation is essential to understand the underlying cellular mechanisms of synaptic plasticity. Long-term potentiation (LTP) and long-term depression (LTD) induced in acute hippocampal slices are widely accepted as cellular models of learning and memory. There are numerous studies that use live cell imaging or immunohistochemistry approaches to visualize activity dependent protein dynamics. However these methods rely on the suitability of antibodies for immunocytochemistry or overexpression of fluorescence-tagged proteins in single neurons. Immunoblotting of proteins is an alternative method providing independent confirmation of the findings. The first limiting factor in preparation of subcellular fractions from individual tetanized hippocampal slices is the low amount of material. Second, the handling procedure is crucial because even very short and minor manipulations of living slices might induce activation of certain signaling cascades. Here we describe an optimized workflow in order to obtain sufficient quantity of nuclear enriched fraction of sufficient purity from the CA1 region of acute hippocampal slices from rat brain. As a representative example we show that the ERK1/2 phosphorylated form of the synapto-nuclear protein messenger Jacob actively translocates to the nucleus upon induction of LTP and can be detected in a nuclear enriched fraction from CA1 neurons.
Karpova, A, Mikhaylova, M, Bera, S, Bär, J, Reddy, PP, Behnisch, T, Rankovic, V, Spilker, C, Bethge, P, Sahin, J, Kaushik, R, Zuschratter, W, Kähne, T, Naumann, M, Gundelfinger, ED & Kreutz, MR 2013, 'Encoding and transducing the synaptic or extrasynaptic origin of NMDA receptor signals to the nucleus', Cell, vol. 152, no. 5, pp. 1119-1133.View/Download from: Publisher's site
The activation of N-methyl-D-aspartate-receptors (NMDARs) in synapses provides plasticity and cell survival signals, whereas NMDARs residing in the neuronal membrane outside synapses trigger neurodegeneration. At present, it is unclear how these opposing signals are transduced to and discriminated by the nucleus. In this study, we demonstrate that Jacob is a protein messenger that encodes the origin of synaptic versus extrasynaptic NMDAR signals and delivers them to the nucleus. Exclusively synaptic, but not extrasynaptic, NMDAR activation induces phosphorylation of Jacob at serine-180 by ERK1/2. Long-distance trafficking of Jacob from synaptic, but not extrasynaptic, sites depends on ERK activity, and association with fragments of the intermediate filament α-internexin hinders dephosphorylation of the Jacob/ERK complex during nuclear transit. In the nucleus, the phosphorylation state of Jacob determines whether it induces cell death or promotes cell survival and enhances synaptic plasticity. © 2013 Elsevier Inc.
Bera, S 2016, 'Activity Dependent Protein Transport from the Synapse to the Nucleus'.