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Glock P., Broichhagen J., Kretschmer S., Blumhardt P., Mücksch J., Trauner D., Schwille P.
(IMPRS-LS students are in bold)
Angew Chem Int Ed Engl, 2017, [Epub ahead of print].
doi: 10.1002/anie.201712002

Optical control of protein pattern formation

Patterns formed by protein reactions and diffusion are the foundation for many phenomena in biology. Yet, the experimental study of reaction-diffusion (R-D) systems has so far been dominated by chemical oscillators, for which many manipulation tools are available. Here, we developed a photoswitch for the Min system of Escherichia coli, a versatile biological in vitro R-D system consisting of the antagonistic proteins MinD and MinE. A MinE-derived peptide of 19 amino acids is covalently modified with a photoisomerizable crosslinker based on azobenzene to externally control peptide-mediated depletion of MinD from the membrane. In addition to providing an on-off switch for pattern formation, we achieve frequency-locked entrainment with a precise 2D spatial memory, allowing new insights into Min protein action on the membrane. Taken together, we provide a tool to externally control protein patterns formed by self-organization.

Albert, S., Schaffer, M., Beck, F., Mosalaganti, S., Asano, S., Thomas, H.F., Plitzko, J.M., Beck, M., Baumeister, W., and Engel, B.D.
Proc Natl Acad Sci USA, 2017, [Epub ahead of print].
doi: 10.1073/pnas.1716305114

Proteasomes tether to two distinct sites at the nuclear pore complex.

The partitioning of cellular components between the nucleus and cytoplasm is the defining feature of eukaryotic life. The nuclear pore complex (NPC) selectively gates the transport of macromolecules between these compartments, but it is unknown whether surveillance mechanisms exist to reinforce this function. By leveraging in situ cryo-electron tomography to image the native cellular environment of Chlamydomonas reinhardtii, we observed that nuclear 26S proteasomes crowd around NPCs. Through a combination of subtomogram averaging and nanometer-precision localization, we identified two classes of proteasomes tethered via their Rpn9 subunits to two specific NPC locations: binding sites on the NPC basket that reflect its eightfold symmetry and more abundant binding sites at the inner nuclear membrane that encircle the NPC. These basket-tethered and membrane-tethered proteasomes, which have similar substrate-processing state frequencies as proteasomes elsewhere in the cell, are ideally positioned to regulate transcription and perform quality control of both soluble and membrane proteins transiting the NPC.

Frauenstein, A., and Meissner, F.
Methods Mol Biol, 2018, 1714, 215-227.
doi: 10.1007/978-1-4939-7519-8_14

Quantitative Proteomics of Secreted Proteins.

Secreted proteins such as cytokines, interleukins, growth factors, and hormones have pleiotropic functions and facilitate intercellular communication in organisms. Quantification of these proteins conventionally relies on antibody-based methods, i.e., enzyme-linked immunosorbent assays (ELISA), whose large-scale use is limited by availability, specificity, and affordability.Here, we describe an experimental and bioinformatics workflow to comprehensively quantify cellular protein secretion by mass spectrometry. Secreted proteins are collected in vitro or ex vivo, digested with proteases and the resulting peptide mixtures are analyzed in single liquid chromatography-mass spectrometry (LC-MS/MS) runs. Label-free quantification and bioinformatics analysis is conducted in the MaxQuant and Perseus computational environment. Our workflow allows the quantification of thousands of secreted proteins spanning a concentration range of four orders of magnitude and permits the systems-level characterization of secretory programs as well as the discovery of proteins with unexpected extracellular functions.

The cerebral cortex is where we learn and think, form impressions of our environment, control conscious behaviour, and store memories. According to the textbooks, the upstream regions of the brain like the thalamus only contribute to these processes by forwarding information from the sensory organs to the corresponding regions of the cerebral cortex and filtering the information, if necessary. Scientists from the Max Planck Institute of Neurobiology have now shown that the textbook account will have to be revised in part. In the mouse brain, at least, the thalamus appears to play a considerably more active role in visual processing in the context of learning than was previously assumed.

A young brain has much to learn – including how it should interpret information from both eyes and collate it into a meaningful image of the environment. Hence, the cells in the visual cortex establish connections with each other during brain development to enable the optimum processing of visual environmental stimuli. In some cases, however, the signals from one eye do not correspond with those from the other eye, for example in children with strabismus. This can result in the incorrect “wiring” of the eyes to the cerebral cortex. The resulting visual weakness can often be corrected by temporarily covering the dominant eye. If this is done during the critical phase for the development of visual processing, the cells alter their connections, and the brain area responsible for the dominant eye receives signals from the uncovered, weaker eye.

The brain can thus learn to process the visual information differently – an insight that is applied successfully through the use of eye patches in children with strabismus. These well-researched processes in the visual cortex have also been used for many years as a model for the study of learning mechanisms in the cerebral cortex based on the example of the mouse brain.

When scientists from Tobias Bonhoeffer’s department examined the activity of neurons from upstream brain areas, in particular the thalamus, during a temporary closure of the eye, they made an astonishing discovery: these cells did not simply relay information from the eyes to the cerebral cortex but also altered their signals in response to the eye closure. “This was completely unexpected, as it has been believed for over 50 years that the thalamus only forwards information and is not actively involved in learning processes,” reports Tobias Rose, leader of the study.

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