Conformation space of a heterodimeric ABC exporter

Cryo-EM has the capacity to capture molecular machines in action. ABC exporters are highly dynamic membrane proteins that extrude a wide range of substances and thereby contribute to essential cellular processes. To reveal how nucleotide binding, hydrolysis, and release are coupled to the conformational dynamics of these proteins, were determined eight high-resolution cryo-EM structures using a conformationally non-selective nanobody. These structures delineate the full functional cycle of an asymmetric ABC exporter in a lipid environment.
Work from the Moeller and Tampé labs in collaboration with the Hummer and Geertsma labs.

Hofmann, Januliene, and Mehdipour et al., 2019

Structural basis for functional interactions in SLC26 dimers

The SLC26 family of transporters maintains anion equilibria in all kingdoms of life. While the only experimental SLC26 structure is monomeric, SLC26 proteins form structural and functional dimers in the lipid membrane. Here we resolve the structure of an SLC26 dimer embedded in a lipid membrane and characterize its functional relevance by combining DEER distance measurements and biochemical studies with MD simulations and spin-label ensemble refinement. Our structural model reveals a unique interface and highlights its functional relevance.
In collaboration with the Hummer and Joseph laboratories.

Chang, Jaumann, and Reichel et al., 2019

Synthetic single domain antibodies for trapping membrane proteins

Mechanistic and structural studies of membrane proteins require their stabilization in specific conformations. Single domain antibodies are potent reagents for this purpose, but their generation relies on immunizations, which impedes selections on challenging targets such as membrane proteins or protein complexes and selections in the presence of ligands typically needed to populate defined conformational states. To overcome this key limitation, we developed an in vitro selection platform based on synthetic single domain antibodies named sybodies.
Work from the Seeger, Dawson, and Geertsma laboratories.

Zimmermann et al., 2018

* joint first author # joint corresponding author

Adrian Pascal Nievergelt#, Dennis R Diener, Aliona Bogdanova, Thomas Brown, Gaia Pigino#
Protocol for precision editing of endogenous Chlamydomonas reinhardtii genes with CRISPR-Cas.
STAR Protoc, 5(1) Art. No. 102774 (2024)
Open Access DOI
CRISPR-Cas genome engineering in the unicellular green algal model Chlamydomonas reinhardtii has until recently suffered from low integration efficiencies despite traditional genetics being well established. Here, we present a protocol for efficient homology-directed knockin mutagenesis in all commonly used strains of Chlamydomonas. We describe steps for scarless integration of fusion tags and sequence modifications of almost all proteins without the need for a preceding mutant line. We further empower this genetic-editing approach by efficient crossing and highly robust screening protocols. For complete details on the use and execution of this protocol, please refer to Nievergelt et al. (2023).1.

Ignacy Rzagalinski, Aliona Bogdanova, Bharath Kumar Raghuraman, Eric R Geertsma, Lena Hersemann, Tjalf Ziemssen, Andrej Shevchenko
FastCAT Accelerates Absolute Quantification of Proteins Using Multiple Short Nonpurified Chimeric Standards.
J Proteome Res, 21(6) 1408-1417 (2022)
Open Access DOI
Absolute (molar) quantification of clinically relevant proteins determines their reference values in liquid and solid biopsies. The FastCAT (for Fast-track QconCAT) method employs multiple short (<50 kDa), stable-isotope labeled chimeric proteins (CPs) composed of concatenated quantotypic (Q)-peptides representing the quantified proteins. Each CP also comprises scrambled sequences of reference (R)-peptides that relate its abundance to a single protein standard (bovine serum albumin, BSA). FastCAT not only alleviates the need to purify CP or use sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) but also improves the accuracy, precision, and dynamic range of the absolute quantification by grouping Q-peptides according to the expected abundance of the target proteins. We benchmarked FastCAT against the reference method of MS Western and tested it in the direct molar quantification of neurological markers in human cerebrospinal fluid at the low ng/mL level.

Roman Renger, Jose A. Morin, Regis P. Lemaitre, Martine Ruer-Gruss, Frank Jülicher, Andreas Hermann, Stephan W. Grill
Co-condensation of proteins with single- and double-stranded DNA.
Proc Natl Acad Sci U.S.A., 119(10) Art. No. e2107871119 (2022)
Open Access DOI
SignificanceBiomolecular condensates are intracellular organelles that are not bounded by membranes and often show liquid-like, dynamic material properties. They typically contain various types of proteins and nucleic acids. How the interaction of proteins and nucleic acids finally results in dynamic condensates is not fully understood. Here we use optical tweezers and fluorescence microscopy to study how the prototypical prion-like protein Fused-in-Sarcoma (FUS) condenses with individual molecules of single- and double-stranded DNA. We find that FUS adsorbs on DNA in a monolayer and hence generates an effectively sticky FUS-DNA polymer that collapses and finally forms a dynamic, reversible FUS-DNA co-condensate. We speculate that protein monolayer-based protein-nucleic acid co-condensation is a general mechanism for forming intracellular membraneless organelles.

Bharath Kumar Raghuraman, Aliona Bogdanova, HongKee Moon, Ignacy Rzagalinski, Eric R Geertsma, Lena Hersemann, Andrej Shevchenko
Median-Based Absolute Quantification of Proteins Using Fully Unlabeled Generic Internal Standard (FUGIS).
J Proteome Res, 21(1) 132-141 (2022)
Open Access DOI
By reporting the molar abundance of proteins, absolute quantification determines their stoichiometry in complexes, pathways, or networks. Typically, absolute quantification relies either on protein-specific isotopically labeled peptide standards or on a semiempirical calibration against the average abundance of peptides chosen from arbitrarily selected proteins. In contrast, a generic protein standard FUGIS (fully unlabeled generic internal standard) requires no isotopic labeling, chemical synthesis, or external calibration and is applicable to quantifying proteins of any organismal origin. The median intensity of the peptide peaks produced by the tryptic digestion of FUGIS is used as a single-point calibrant to determine the molar abundance of any codigested protein. Powered by FUGIS, median-based absolute quantification (MBAQ) outperformed other methods of untargeted proteome-wide absolute quantification.

Juliana G. Roscito, Kaushikaram Subramanian, Ronald Naumann, Mihail Sarov, Anna Shevchenko, Aliona Bogdanova, Thomas Kurth, Leo Foerster, Moritz Kreysing, Michael Hiller
Recapitulating evolutionary divergence in a single cis-regulatory element is sufficient to cause expression changes of the lens gene Tdrd7.
Mol Biol Evol, 38(2) 380-392 (2020)
Open Access PDF DOI
Mutations in cis-regulatory elements play important roles for phenotypic changes during evolution. Eye degeneration in the blind mole rat (BMR; Nannospalax galili) and other subterranean mammals is significantly associated with widespread divergence of eye regulatory elements, but the effect of these regulatory mutations on eye development and function has not been explored. Here, we investigate the effect of mutations observed in the BMR sequence of a conserved non-coding element upstream of Tdrd7, a pleiotropic gene required for lens development and spermatogenesis. We first show that this conserved element is a transcriptional repressor in lens cells and that the BMR sequence partially lost repressor activity. Next, we recapitulated evolutionary changes in this element by precisely replacing the endogenous regulatory element in a mouse line by the orthologous BMR sequence with CRISPR-Cas9. Strikingly, this repressor replacement caused a more than two-fold up-regulation of Tdrd7 in the developing lens; however, increased mRNA level does not result in a corresponding increase in TDRD7 protein nor an obvious lens phenotype, possibly explained by buffering at the posttranscriptional level. Our results are consistent with eye degeneration in subterranean mammals having a polygenic basis where many small-effect mutations in different eye-regulatory elements collectively contribute to phenotypic differences.

Elisabeth Nüske, Guendalina Marini, Doris Richter, Weihua Leng, Aliona Bogdanova, Titus Franzmann, Gaia Pigino, Simon Alberti
Filament formation by the translation factor eIF2B regulates protein synthesis in starved cells.
Biol Open, 9(7) Art. No. bio.046391 (2020)
Open Access DOI
Cells exposed to starvation have to adjust their metabolism to conserve energy and protect themselves. Protein synthesis is one of the major energy-consuming processes and as such has to be tightly controlled. Many mechanistic details about how starved cells regulate the process of protein synthesis are still unknown. Here, we report that the essential translation initiation factor eIF2B forms filaments in starved budding yeast cells. We demonstrate that filamentation is triggered by starvation-induced acidification of the cytosol, which is caused by an influx of protons from the extracellular environment. We show that filament assembly by eIF2B is necessary for rapid and efficient downregulation of translation. Importantly, this mechanism does not require the kinase Gcn2. Furthermore, analysis of site-specific variants suggests that eIF2B assembly results in enzymatically inactive filaments that promote stress survival and fast recovery of cells from starvation. We propose that translation regulation through filament assembly is an efficient mechanism that allows yeast cells to adapt to fluctuating environments.

Takashi Namba#, Judit Dóczi, Anneline Pinson, Lei Xing, Nereo Kalebic, Michaela Wilsch-Bräuninger, Katherine S. Long, Samir Vaid, Janelle Lauer, Aliona Bogdanova, Barbara Borgonovo, Anna Shevchenko, Patrick Keller, David N. Drechsel, Teymuras V. Kurzchalia, Pauline Wimberger, Christos Chinopoulos, Wieland Huttner#
Human-Specific ARHGAP11B Acts in Mitochondria to Expand Neocortical Progenitors by Glutaminolysis.
Neuron, 105(5) 867-881 (2020)
The human-specific gene ARHGAP11B is preferentially expressed in neural progenitors of fetal human neocortex and increases abundance and proliferation of basal progenitors (BPs), which have a key role in neocortex expansion. ARHGAP11B has therefore been implicated in the evolutionary expansion of the human neocortex, but its mode of action has been unknown. Here, we show that ARHGAP11B is imported into mitochondria, where it interacts with the adenine nucleotide translocase (ANT) and inhibits the mitochondrial permeability transition pore (mPTP). BP expansion by ARHGAP11B requires its presence in mitochondria, and pharmacological inhibition of ANT function or mPTP opening mimic BP expansion by ARHGAP11B. Searching for the underlying metabolic basis, we find that BP expansion by ARHGAP11B requires glutaminolysis, the conversion of glutamine to glutamate for the tricarboxylic acid (TCA) cycle. Hence, an ARHGAP11B-induced, mitochondria-based effect on BP metabolism that is a hallmark of highly mitotically active cells appears to underlie its role in neocortex expansion.

Regis P. Lemaitre, Aliona Bogdanova, Barbara Borgonovo, Jeffrey Woodruff#, David N. Drechsel#
FlexiBAC: a versatile, open-source baculovirus vector system for protein expression, secretion, and proteolytic processing.
BMC Biotechnol., 19(1) Art. No. 20 (2019)
Open Access DOI
Baculovirus-mediated expression in insect cells is a powerful approach for protein production. However, many existing methods are time-consuming, offer limited options for protein tagging, and are unsuitable for secreted proteins requiring proteolytic maturation, such as TGF-β family growth factors.

Martina Rauner✳︎, Ulrike Baschant✳︎, Antonella Roetto, Rosa Maria Pellegrino, Sandra Rother, Juliane Salbach-Hirsch, Heike Weidner, Vera Hintze, Graeme Campbell, Andreas Petzold, Regis P. Lemaitre, Ian Henry, Teresita Bellido, Igor Theurl, Sandro Altamura, Silvia Colucci, Martina Muckenthaler, Georg Schett, Davide Komla Ebri, J H Duncan Bassett, Graham R Williams, Uwe Platzbecker, Lorenz C Hofbauer
Transferrin receptor 2 controls bone mass and pathological bone formation via BMP and Wnt signaling.
Nat Metab, 1(1) 111-124 (2019)
Transferrin receptor 2 (Tfr2) is mainly expressed in the liver and controls iron homeostasis. Here, we identify Tfr2 as a regulator of bone homeostasis that inhibits bone formation. Mice lacking Tfr2 display increased bone mass and mineralization independent of iron homeostasis and hepatic Tfr2. Bone marrow transplantation experiments and studies of cell-specific Tfr2 knockout mice demonstrate that Tfr2 impairs BMP-p38MAPK signaling and decreases expression of the Wnt inhibitor sclerostin specifically in osteoblasts. Reactivation of MAPK or overexpression of sclerostin rescues skeletal abnormalities in Tfr2 knockout mice. We further show that the extracellular domain of Tfr2 binds BMPs and inhibits BMP-2-induced heterotopic ossification by acting as a decoy receptor. These data indicate that Tfr2 limits bone formation by modulating BMP signaling, possibly through direct interaction with BMP either as a receptor or as a co-receptor in a complex with other BMP receptors. Finally, the Tfr2 extracellular domain may be effective in the treatment of conditions associated with pathological bone formation.

Jun Hoe Lee, Kevin M Lewis, Timothy W Moural, Bogdan Kirilenko, Barbara Borgonovo, Gisa Prange, Manfred Koessl, Stefan Huggenberger, ChulHee Kang, Michael Hiller
Molecular parallelism in fast-twitch muscle proteins in echolocating mammals
Sci Adv, 4(9) Art. No. eaat9660 (2018)
Open Access PDF DOI

Peggy Stolt-Bergner, Christian Benda, Tim Bergbrede, Hüseyin Besir, Patrick H N Celie, Cindy Chang, David N. Drechsel, Ariane Fischer, Arie Geerlof, Barbara Giabbai, Joop van den Heuvel, Georg Huber, Wolfgang Knecht, Anita Lehner, Regis P. Lemaitre, Kristina Nordén, Gwynn Pardee, Ines Racke, Kim Remans, Astrid Sander, Judith Scholz, Magda Stadnik, Paola Storici, Daniel Weinbruch, Isabel Zaror, Linda H L Lua, Sabine Suppmann
Baculovirus-driven protein expression in insect cells: A benchmarking study.
J Struct Biol, 203(2) 71-80 (2018)
Baculovirus-insect cell expression system has become one of the most widely used eukaryotic expression systems for heterologous protein production in many laboratories. The availability of robust insect cell lines, serum-free media, a range of vectors and commercially-packaged kits have supported the demand for maximizing the exploitation of the baculovirus-insect cell expression system. Naturally, this resulted in varied strategies adopted by different laboratories to optimize protein production. Most laboratories have preference in using either the E. coli transposition-based recombination bacmid technology (e.g. Bac-to-Bac®) or homologous recombination transfection within insect cells (e.g. flashBAC™). Limited data is presented in the literature to benchmark the protocols used for these baculovirus vectors to facilitate the selection of a system for optimal production of target proteins. Taking advantage of the Protein Production and Purification Partnership in Europe (P4EU) scientific network, a benchmarking initiative was designed to compare the diverse protocols established in thirteen individual laboratories. This benchmarking initiative compared the expression of four selected intracellular proteins (mouse Dicer-2, 204 kDa; human ABL1 wildtype, 126 kDa; human FMRP, 68 kDa; viral vNS1-H1, 76 kDa). Here, we present the expression and purification results on these proteins and highlight the significant differences in expression yields obtained using different commercially-packaged baculovirus vectors. The highest expression level for difficult-to-express intracellular protein candidates were observed with the EmBacY baculovirus vector system.

Mukesh Kumar, Shai Joseph, Martina Augsburg, Aliona Bogdanova, David N. Drechsel, Nadine Vastenhouw, Frank Buchholz, Marc Gentzel, Andrej Shevchenko
MS Western, a Method of Multiplexed Absolute Protein Quantification is a Practical Alternative to Western Blotting.
Mol Cell Proteomics, 17(2) 384-396 (2018)
Open Access DOI
Absolute quantification of proteins elucidates the molecular composition, regulation and dynamics of multiprotein assemblies and networks. Here we report on a method termed MS Western that accurately determines the molar abundance of dozens of user-selected proteins at the subfemtomole level in whole cell or tissue lysates without metabolic or chemical labeling and without using specific antibodies. MS Western relies on GeLC-MS/MS and quantifies proteins by in-gel codigestion with an isotopically labeled QconCAT protein chimera composed of concatenated proteotypic peptides. It requires no purification of the chimera and relates the molar abundance of all proteotypic peptides to a single reference protein. In comparative experiments, MS Western outperformed immunofluorescence Western blotting by the protein detection specificity, linear dynamic range and sensitivity of protein quantification. To validate MS Western in an in vivo experiment, we quantified the molar content of zebrafish core histones H2A, H2B, H3 and H4 during ten stages of early embryogenesis. Accurate quantification (CV<10%) corroborated the anticipated histones equimolar stoichiometry and revealed an unexpected trend in their total abundance.

Catarina Oliveira, Regis P. Lemaitre, Prayag Murawala, Akira Tazaki, David N. Drechsel, Elly M. Tanaka
Pseudotyped baculovirus is an effective gene expression tool for studying molecular function during axolotl limb regeneration.
Dev Biol, 433(2) 262-275 (2018)
Axolotls can regenerate complex structures through recruitment and remodeling of cells within mature tissues. Accessing the underlying mechanisms at a molecular resolution is crucial to understand how injury triggers regeneration and how it proceeds. However, gene transformation in adult tissues can be challenging. Here we characterize the use of pseudotyped baculovirus (BV) as an effective gene transfer method both for cells within mature limb tissue and within the blastema. These cells remain competent to participate in regeneration after transduction. We further characterize the effectiveness of BV for gene overexpression studies by overexpressing Shh in the blastema, which yields a high penetrance of classic polydactyly phenotypes. Overall, our work establishes BV as a powerful tool to access gene function in axolotl limb regeneration.

Jifeng Fei, Maritta Schuez, Dunja Knapp, Yuka Taniguchi, David N. Drechsel, Elly M. Tanaka
Efficient gene knockin in axolotl and its use to test the role of satellite cells in limb regeneration.
Proc Natl Acad Sci U.S.A., 114(47) 12501-12506 (2017)
Salamanders exhibit extensive regenerative capacities and serve as a unique model in regeneration research. However, due to the lack of targeted gene knockin approaches, it has been difficult to label and manipulate some of the cell populations that are crucial for understanding the mechanisms underlying regeneration. Here we have established highly efficient gene knockin approaches in the axolotl (Ambystoma mexicanum) based on the CRISPR/Cas9 technology. Using a homology-independent method, we successfully inserted both the Cherry reporter gene and a larger membrane-tagged Cherry-ERT2-Cre-ERT2 (∼5-kb) cassette into axolotl Sox2 and Pax7 genomic loci. Depending on the size of the DNA fragments for integration, 5-15% of the F0 transgenic axolotl are positive for the transgene. Using these techniques, we have labeled and traced the PAX7-positive satellite cells as a major source contributing to myogenesis during axolotl limb regeneration. Our work brings a key genetic tool to molecular and cellular studies of axolotl regeneration.

Tobias Boothe, Lennart Hilbert, Michael Heide, Lea Berninger, Wieland B. Huttner, Vasily Zaburdaev, Nadine Vastenhouw, Eugene W Myers, David N. Drechsel, Jochen Rink
A tunable refractive index matching medium for live imaging cells, tissues and model organisms.
Elife, 6 Art. No. e27240 (2017)
Open Access DOI
In light microscopy, refractive index mismatches between media and sample cause spherical aberrations that often limit penetration depth and resolution. Optical clearing techniques can alleviate these mismatches, but they are so far limited to fixed samples. We present Iodixanol as a non-toxic medium supplement that allows refractive index matching in live specimens and thus substantially improves image quality in live-imaged primary cell cultures, planarians, zebrafish and human cerebral organoids.

Jovan Mircetic, Iris Steinebrunner, Li Ding, Jifeng Fei, Aliona Bogdanova, David N. Drechsel, Frank Buchholz
Purified Cas9 Fusion Proteins for Advanced Genome Manipulation.
Small Methods, 1(4) Art. No. 1600052 (2017)
The CRISPR/Cas9 system (CRISPR = clustered regularly interspaced short palindromic repeats) has rapidly become one of the most versatile genome manipulation technologies, and different methods to introduce the Cas9 nuclease activity into cells have been developed. The direct delivery of purified Cas9 protein complexed with a guide RNA as a ribonucleoprotein (RNP) has emerged as an advantageous approach, as it provides instant, but limited activity of the enzyme, thereby reducing off-target cleavage. The usefulness of the CRISPR/Cas9 system has recently been extended by the generation of Cas9 or dead (d) Cas9 fusion genes. However, these systems have so far been mainly explored when delivered by expression plasmids. Here, a variety of purified Cas9 fusion proteins are generated, and their utility is tested in a number of assays. This work illustrates that Cas9 fused to green-or redfluorescent proteins can be usefully employed to increase the frequency of targeted cells when transfected as RNPs. Furthermore, it is demonstrated that purified dCas9 fused to a dual transactivation domain can potently activate gene expression when transfected as an RNP into embryonic stem cells. The results show that purified Cas9 fusion proteins are versatile and efficient reagents that facilitate advanced genome manipulation.

Ines Wagner✳︎, Heng Wang, Philipp M Weissert, Werner L Straube✳︎, Anna Shevchenko, Marc Gentzel, Goncalo Brito, Akira Tazaki, Catarina Oliveira, Takuji Sugiura, Andrej Shevchenko, András Simon, David N. Drechsel, Elly M. Tanaka
Serum Proteases Potentiate BMP-Induced Cell Cycle Re-entry of Dedifferentiating Muscle Cells during Newt Limb Regeneration.
Dev Cell, 40(6) 608-617 (2017)
Limb amputation in the newt induces myofibers to dedifferentiate and re-enter the cell cycle to generate proliferative myogenic precursors in the regeneration blastema. Here we show that bone morphogenetic proteins (BMPs) and mature BMPs that have been further cleaved by serum proteases induce cell cycle entry by dedifferentiating newt muscle cells. Protease-activated BMP4/7 heterodimers that are present in serum strongly induced myotube cell cycle re-entry with protease cleavage yielding a 30-fold potency increase of BMP4/7 compared with canonical BMP4/7. Inhibition of BMP signaling via muscle-specific dominant-negative receptor expression reduced cell cycle entry in vitro and in vivo. In vivo inhibition of serine protease activity depressed cell cycle re-entry, which in turn was rescued by cleaved-mimic BMP. This work identifies a mechanism of BMP activation that generates blastema cells from differentiated muscle.

Elvan Boke, Martine Ruer, Martin Wühr, Margaret Coughlin, Regis P. Lemaitre, Steven Gygi, Simon Alberti, David N. Drechsel, Anthony Hyman, Timothy J. Mitchison
Amyloid-like Self-Assembly of a Cellular Compartment.
Cell, 166(3) 637-650 (2016)
Most vertebrate oocytes contain a Balbiani body, a large, non-membrane-bound compartment packed with RNA, mitochondria, and other organelles. Little is known about this compartment, though it specifies germline identity in many non-mammalian vertebrates. We show Xvelo, a disordered protein with an N-terminal prion-like domain, is an abundant constituent of Xenopus Balbiani bodies. Disruption of the prion-like domain of Xvelo, or substitution with a prion-like domain from an unrelated protein, interferes with its incorporation into Balbiani bodies in vivo. Recombinant Xvelo forms amyloid-like networks in vitro. Amyloid-like assemblies of Xvelo recruit both RNA and mitochondria in binding assays. We propose that Xenopus Balbiani bodies form by amyloid-like assembly of Xvelo, accompanied by co-recruitment of mitochondria and RNA. Prion-like domains are found in germ plasm organizing proteins in other species, suggesting that Balbiani body formation by amyloid-like assembly could be a conserved mechanism that helps oocytes function as long-lived germ cells.

Eugeniu Nacu, Elena Gromberg, Catarina Oliveira, David N. Drechsel, Elly M. Tanaka
FGF8 and SHH substitute for anterior-posterior tissue interactions to induce limb regeneration.
Nature, 533(7603) 407-410 (2016)
In salamanders, grafting of a left limb blastema onto a right limb stump yields regeneration of three limbs, the normal limb and two 'supernumerary' limbs. This experiment and other research have shown that the juxtaposition of anterior and posterior limb tissue plus innervation are necessary and sufficient to induce complete limb regeneration in salamanders. However, the cellular and molecular basis of the requirement for anterior-posterior tissue interactions were unknown. Here we have clarified the molecular basis of the requirement for both anterior and posterior tissue during limb regeneration and supernumerary limb formation in axolotls (Ambystoma mexicanum). We show that the two tissues provide complementary cross-inductive signals that are required for limb outgrowth. A blastema composed solely of anterior tissue normally regresses rather than forming a limb, but activation of hedgehog (HH) signalling was sufficient to drive regeneration of an anterior blastema to completion owing to its ability to maintain fibroblast growth factor (FGF) expression, the key signalling activity responsible for blastema outgrowth. In blastemas composed solely of posterior tissue, HH signalling was not sufficient to drive regeneration; however, ectopic expression of FGF8 together with endogenous HH signalling was sufficient. In axolotls, FGF8 is expressed only in the anterior mesenchyme and maintenance of its expression depends on sonic hedgehog (SHH) signalling from posterior tissue. Together, our findings identify key anteriorly and posteriorly localized signals that promote limb regeneration and show that these single factors are sufficient to drive non-regenerating blastemas to complete regeneration with full elaboration of skeletal elements.

Anneke Hibbel, Aliona Bogdanova, Mohammed Mahamdeh, Anita Jannasch, Marko Storch, Erik Schäffer, Dimitris Liakopoulos, Jonathon Howard
Kinesin Kip2 enhances microtubule growth in vitro through length-dependent feedback on polymerization and catastrophe.
Elife, 4 Art. No. e10542 (2015)
Open Access PDF DOI
The size and position of mitotic spindles is determined by the lengths of their constituent microtubules. Regulation of microtubule length requires feedback to set the balance between growth and shrinkage. Whereas negative feedback mechanisms for microtubule length control, based on depolymerizing kinesins and severing proteins, have been studied extensively, positive feedback mechanisms are not known. Here we report that the budding yeast kinesin Kip2 is a microtubule polymerase and catastrophe inhibitor in vitro that uses its processive motor activity as part of a feedback loop to further promote microtubule growth. Positive feedback arises because longer microtubules bind more motors, which walk to the ends where they further reinforce growth and inhibit catastrophe. We propose that positive feedback, common in biochemical pathways to switch between signaling states, can also be used in a mechanical signaling pathway to switch between structural states, in this case between short and long polymers.

Avinash Patel, Hyun-Ok Kate Lee, Louise Jawerth, Shovamayee Maharana, Marcus Jahnel, Marco Y Hein, Stoyno Stoynov, Julia Mahamid, Shambaditya Saha, Titus Franzmann, Andrei Pozniakovski, Ina Poser, Nicola Maghelli, Loic Royer, Martin Weigert, Eugene W Myers, Stephan W. Grill, David N. Drechsel, Anthony Hyman, Simon Alberti
A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation.
Cell, 162(5) 1066-1077 (2015)
Many proteins contain disordered regions of low-sequence complexity, which cause aging-associated diseases because they are prone to aggregate. Here, we study FUS, a prion-like protein containing intrinsically disordered domains associated with the neurodegenerative disease ALS. We show that, in cells, FUS forms liquid compartments at sites of DNA damage and in the cytoplasm upon stress. We confirm this by reconstituting liquid FUS compartments in vitro. Using an in vitro "aging" experiment, we demonstrate that liquid droplets of FUS protein convert with time from a liquid to an aggregated state, and this conversion is accelerated by patient-derived mutations. We conclude that the physiological role of FUS requires forming dynamic liquid-like compartments. We propose that liquid-like compartments carry the trade-off between functionality and risk of aggregation and that aberrant phase transitions within liquid-like compartments lie at the heart of ALS and, presumably, other age-related diseases. VIDEO ABSTRACT.

Robert Wieduwild, Swati Krishnan, Karolina Chwalek, Annett Boden, Matthias Nowak, David N. Drechsel, Carsten Werner, Yixin Zhang
Noncovalent hydrogel beads as microcarriers for cell culture.
Angew Chem Int Ed Engl, 54(13) 3962-3966 (2015)
Hydrogel beads as microcarriers could have many applications in biotechnology. However, bead formation by noncovalent cross-linking to achieve high cell compatibility by avoiding chemical reactions remains challenging because of rapid gelation rates and/or low stability. Here we report the preparation of homogeneous, tunable, and robust hydrogel beads from peptide-polyethylene glycol conjugates and oligosaccharides under mild, cell-compatible conditions using a noncovalent crosslinking mechanism. Large proteins can be released from beads easily. Further noncovalent modification allows for bead labeling and functionalization with various compounds. High survival rates of embedded cells were achieved under standard cell culture conditions and after freezing the beads, demonstrating its suitability for encapsulating and conserving cells. Hydrogel beads as functional system have been realized by generating protein-producing microcarriers with embedded eGFP-secreting insect cells.

Juha M. Torkko, María E Primo, Ronald Dirkx, Anne Friedrich, Antje Viehrig, Elisa Vergari, Barbara Borgonovo, Anke Sönmez, Carolin Wegbrod, Martina Lachnit, Carla Münster, Mauricio P Sica, Mario R Ermácora, Michele Solimena
Stability of proICA512/IA-2 and Its Targeting to Insulin Secretory Granules Require β4-Sheet-Mediated Dimerization of Its Ectodomain in the Endoplasmic Reticulum.
Mol Cell Biol, 35(6) 914-927 (2015)
The type 1 diabetes autoantigen ICA512/IA-2/RPTPN is a receptor protein tyrosine phosphatase of the insulin secretory granules (SGs) which regulates the size of granule stores, possibly via cleavage/signaling of its cytosolic tail. The role of its extracellular region remains unknown. Structural studies indicated that β2- or β4-strands in the mature ectodomain (ME ICA512) form dimers in vitro. Here we show that ME ICA512 prompts proICA512 dimerization in the endoplasmic reticulum. Perturbation of ME ICA512 β2-strand N-glycosylation upon S508A replacement allows for proICA512 dimerization, O-glycosylation, targeting to granules, and conversion, which are instead precluded upon G553D replacement in the ME ICA512 β4-strand. S508A/G553D and N506A/G553D double mutants dimerize but remain in the endoplasmic reticulum. Removal of the N-terminal fragment (ICA512-NTF) preceding ME ICA512 allows an ICA512-ΔNTF G553D mutant to exit the endoplasmic reticulum, and ICA512-ΔNTF is constitutively delivered to the cell surface. The signal for SG sorting is located within the NTF RESP18 homology domain (RESP18-HD), whereas soluble NTF is retained in the endoplasmic reticulum. Hence, we propose that the ME ICA512 β2-strand fosters proICA512 dimerization until NTF prevents N506 glycosylation. Removal of this constraint allows for proICA512 β4-strand-induced dimerization, exit from the endoplasmic reticulum, O-glycosylation, and RESP18-HD-mediated targeting to granules.

Per Widlund, Marija Podolski, Simone Reber, Joshua Alper, Marko Storch, Anthony Hyman, Jonathon Howard, David N. Drechsel
One-step purification of assembly-competent tubulin from diverse eukaryotic sources.
Mol Biol Cell, 23(22) 4393-4401 (2012)
We have developed a protocol that allows rapid and efficient purification of native, active tubulin from a variety of species and tissue sources by affinity chromatography. The affinity matrix comprises a bacterially expressed, recombinant protein, the TOG1/2 domains from Saccharomyces cerevisiae Stu2, covalently coupled to a Sepharose support. The resin has a high capacity to specifically bind tubulin from clarified crude cell extracts, and, after washing, highly purified tubulin can be eluted under mild conditions. The eluted tubulin is fully functional and can be efficiently assembled into microtubules. The method eliminates the need to use heterologous systems for the study of microtubule-associated proteins and motor proteins, which has been a major issue in microtubule-related research.

Aurelie Tomczak, Jana Sontheimer, David N. Drechsel, Rainer Hausdorf, Marc Gentzel, Andrej Shevchenko, Stefanie Eichler, Karim Fahmy, Frank Buchholz, Maria Teresa Pisabarro
3D profile-based approach to proteome-wide discovery of novel human chemokines
PLoS ONE, 7(5) Art. No. e36151 (2012)
Chemokines are small secreted proteins with important roles in immune responses. They consist of a conserved three-dimensional (3D) structure, so-called IL8-like chemokine fold, which is supported by disulfide bridges characteristic of this protein family. Sequence- and profile-based computational methods have been proficient in discovering novel chemokines by making use of their sequence-conserved cysteine patterns. However, it has been recently shown that some chemokines escaped annotation by these methods due to low sequence similarity to known chemokines and to different arrangement of cysteines in sequence and in 3D. Innovative methods overcoming the limitations of current techniques may allow the discovery of new remote homologs in the still functionally uncharacterized fraction of the human genome. We report a novel computational approach for proteome-wide identification of remote homologs of the chemokine family that uses fold recognition techniques in combination with a scaffold-based automatic mapping of disulfide bonds to define a 3D profile of the chemokine protein family. By applying our methodology to all currently uncharacterized human protein sequences, we have discovered two novel proteins that, without having significant sequence similarity to known chemokines or characteristic cysteine patterns, show strong structural resemblance to known anti-HIV chemokines. Detailed computational analysis and experimental structural investigations based on mass spectrometry and circular dichroism support our structural predictions and highlight several other chemokine-like features. The results obtained support their functional annotation as putative novel chemokines and encourage further experimental characterization. The identification of remote homologs of human chemokines may provide new insights into the molecular mechanisms causing pathologies such as cancer or AIDS, and may contribute to the development of novel treatments. Besides, the genome-wide applicability of our methodology based on 3D protein family profiles may open up new possibilities for improving and accelerating protein function annotation processes.

Uenal Coskun, Michal Grzybek, Kai Simons, David N. Drechsel
Regulation of human EGF receptor by lipids
Proc Natl Acad Sci U.S.A., 108(22) 9044-9048 (2011)

Christopher Gell, Claire Friel, Barbara Borgonovo, David N. Drechsel, Anthony A. Hyman, Jonathon Howard
Purification of tubulin from porcine brain.
Methods Mol Biol, 777 15-28 (2011)
Microtubules, polymers of the heterodimeric protein αβ-tubulin, give shape to cells and are the tracks for vesicle transport and chromosome segregation. In vitro assays to study microtubule functions and their regulation by microtubule-associated proteins require the availability of purified αβ-tubulin. In this chapter, we describe the process of purification of heterodimeric αβ-tubulin from porcine brain.

Lars Renner, Tilo Pompe, Regis P. Lemaitre, David N. Drechsel, Carsten Werner
Controlled enhancement of transmembrane enzyme activity in polymer cushioned supported bilayer membranes
Soft Matter, 6 5382-5389 (2010)
Reconstitution of transmembrane proteins into supported lipid bilayer (SLB) membranes has often been hampered by strong interactions of protein domains with the underlying solid support leading to loss of both activity and mobility within the plane of the lipid bilayer. Polymer cushioned SLBs can overcome this by avoiding direct contact with the support. To extend this approach we developed an anionic polymer cushion system that allows tunable lipid mobility as well as functional integration of the transmembrane protein β-amyloid precursor protein cleaving enzyme (BACE) into SLBs. Fluorescence recovery after photobleaching analysis revealed a homogeneous distribution and high lateral mobility of the reconstituted BACE in cushioned SLBs while an impaired mobility and inhomogeneous clustering of reconstituted BACE were found in SLBs on silicon oxide substrates. The cushioning of SLBs led to increased incorporation and enhanced enzymatic activity of the reconstituted BACE with a direct correlation between lipid mobility and BACE activity. The utilized polymer cushion system allows the successful reconstitution of transmembrane proteins within SLBs with tunable properties.

Takeshi Ohya, Marta Miaczynska, Uenal Coskun, Barbara Lommer, Anja Runge, David N. Drechsel, Yannis Kalaidzidis, Marino Zerial
Reconstitution of Rab- and SNARE-dependent membrane fusion by synthetic endosomes.
Nature, 459(7250) 1091-1097 (2009)
Rab GTPases and SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) are evolutionarily conserved essential components of the eukaryotic intracellular transport system. Although pairing of cognate SNAREs is sufficient to fuse membranes in vitro, a complete reconstitution of the Rab-SNARE machinery has never been achieved. Here we report the reconstitution of the early endosomal canine Rab5 GTPase, its key regulators and effectors together with SNAREs into proteoliposomes using a set of 17 recombinant human proteins. These vesicles behave like minimal 'synthetic' endosomes, fusing with purified early endosomes or with each other in vitro. Membrane fusion measured by content-mixing and morphological assays requires the cooperativity between Rab5 effectors and cognate SNAREs which, together, form a more efficient 'core machinery' than SNAREs alone. In reconstituting a fusion mechanism dependent on both a Rab GTPase and SNAREs, our work shows that the two machineries act coordinately to increase the specificity and efficiency of the membrane tethering and fusion process.

Sara Lööf, Werner L. Straube, David N. Drechsel, Elly M. Tanaka, András Simon
Plasticity of mammalian myotubes upon stimulation with a thrombin-activated serum factor.
Cell Cycle, 6(9) 1096-1101 (2007)
Salamanders display unique regeneration abilities among adult vertebrates. An intriguing feature of salamander regeneration is the dedifferentiation of cells, such as myofibers and myotubes at the injury site, a process that involves cell cycle reentry from the differentiated state. A thrombin-activated serum factor that is distinct from conventional growth factors is known to cause S-phase reentry in salamander myotubes. While mammalian myotubes do not reenter S-phase upon serum stimulation, an upregulation of some immediate early genes such as jun and fos has been observed. Until now, it was unknown whether this transcriptional response was stimulated by conventional growth factors or by the thrombin-activated serum factor. By measuring transcriptional activity in individually purified C2C12 mouse myotubes using quantitative reverse transcription polymerase chain reactions, we show that a set of immediate early genes are activated in response to the thrombin-activated serum factor in a distinct manner from the growth factors PDGF, FGF and EGF. A partially purified fraction of the thrombin activated serum factor elicited stronger upregulation of a broader set of genes compared to individual growth factors and additionally caused downregulation of E2F6. Despite this robust transcriptional response in mammalian myotubes, we did not detect a large-scale change in histone H3K9 di-methylation or S-phase, a feature that characterizes salamander serum-stimulated myotubes. Our results indicate that mammalian myotubes have retained responsiveness to the thrombin-activated serum factor, but full reentry into S-phase is prevented by factors downstream of the immediate early genes.

Nicola Bauer
New insights into the plasma membrane dynamics of rare stem cells by studying the prominin molecule
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2007)

Hassan Mziaut, Mirko Trajkovski, Stephan Kersting, Armin Ehninger, Anke Altkrüger, Regis P. Lemaitre, Darja Schmidt, Hans-Detlev Saeger, Myung-Shik Lee, David N. Drechsel, Stefan Müller, Michele Solimena
Synergy of glucose and growth hormone signalling in islet cells through ICA512 and STAT5.
Nat Cell Biol, 8(5) 435-445 (2006)
Nutrients and growth hormones promote insulin production and the proliferation of pancreatic beta-cells. An imbalance between ever-increasing metabolic demands and insulin output causes diabetes. Recent evidence indicates that beta-cells enhance insulin gene expression depending on their secretory activity. This signalling pathway involves a catalytically inactive receptor tyrosine phosphatase, ICA512, whose cytoplasmic tail is cleaved on glucose-stimulated exocytosis of insulin secretory granules and then moves into the nucleus, where it upregulates insulin transcription. Here, we show that the cleaved cytosolic fragment of ICA512 enhances the transcription of secretory granule genes (including its own gene) by binding to tyrosine phosphorylated signal transducers and activators of transcription (STAT) 5 and preventing its dephosphorylation. Sumoylation of ICA512 by the E3 SUMO ligase PIASy, in turn, may reverse this process by decreasing the binding of ICA512 to STAT5. These findings illustrate how the exocytosis of secretory granules, through a retrograde pathway that sustains STAT activity, converges with growth hormone signalling to induce adaptive changes in beta-cells in response to metabolic demands.

Gideon Lansbergen, Yulia Komarova, Mauro Modesti, Claire Wyman, Casper C Hoogenraad, Holly V Goodson, Regis P. Lemaitre, David N. Drechsel, Erik van Munster, Theodorus W J Gadella, Frank Grosveld, Niels Galjart, Gary G Borisy, Anna Akhmanova
Conformational changes in CLIP-170 regulate its binding to microtubules and dynactin localization.
J Cell Biol, 166(7) 1003-1014 (2004)
Cytoplasmic linker protein (CLIP)-170, CLIP-115, and the dynactin subunit p150(Glued) are structurally related proteins, which associate specifically with the ends of growing microtubules (MTs). Here, we show that down-regulation of CLIP-170 by RNA interference results in a strongly reduced accumulation of dynactin at the MT tips. The NH(2) terminus of p150(Glued) binds directly to the COOH terminus of CLIP-170 through its second metal-binding motif. p150(Glued) and LIS1, a dynein-associating protein, compete for the interaction with the CLIP-170 COOH terminus, suggesting that LIS1 can act to release dynactin from the MT tips. We also show that the NH(2)-terminal part of CLIP-170 itself associates with the CLIP-170 COOH terminus through its first metal-binding motif. By using scanning force microscopy and fluorescence resonance energy transfer-based experiments we provide evidence for an intramolecular interaction between the NH(2) and COOH termini of CLIP-170. This interaction interferes with the binding of the CLIP-170 to MTs. We propose that conformational changes in CLIP-170 are important for binding to dynactin, LIS1, and the MT tips.

Nnennaya Kanu, Yutaka Imokawa, David N. Drechsel, R Anthony Williamson, Christopher R Birkett, Christopher J Bostock, Jeremy P. Brockes
Transfer of scrapie prion infectivity by cell contact in culture.
Curr Biol, 12(7) 523-530 (2002)
BACKGROUND: When a cell is infected with scrapie prions, newly synthesized molecules of the prion protein PrP(C) are expressed at the cell surface and may subsequently be converted to the abnormal form PrP(Sc). In an experimental scrapie infection of an animal, the initial innoculum of PrP(Sc) is cleared relatively rapidly, and the subsequent propagation of the infection depends on the ability of infected cells to convert uninfected target cells to stable production of PrP(Sc). The mechanism of such cell-based infection is not understood. RESULTS: We have established a system in dissociated cell culture in which scrapie-infected mouse SMB cells are able to stably convert genetically marked target cells by coculture. After coculture and rigorous removal of SMB cells, the target cells express PrP(Sc) and also incorporate [35S]methionine into PrP(Sc). The extent of conversion was sensitive to the ratio of the two cell types, and conversion by live SMB required 2500-fold less PrP(Sc) than conversion by a cell-free prion preparation. The conversion activity of SMB cells is not detectable in conditioned medium and apparently depends on close proximity or contact, as evidenced by culturing the SMB and target cells on neighboring but separate surfaces. SMB cells were killed by fixation in aldehydes, followed by washing, and were found to retain significant activity at conversion of target cells. CONCLUSIONS: Cell-mediated infection of target cells in this culture system is effective and requires significantly less PrP(Sc) than infection by a prion preparation. Several lines of evidence indicate that it depends on cell contact, in particular, the activity of aldehyde-fixed infected cells.

Elly M. Tanaka, David N. Drechsel, Jeremy P. Brockes
Thrombin regulates S-phase re-entry by cultured newt myotubes.
Curr Biol, 9(15) 792-799 (1999)
BACKGROUND: Adult urodele amphibians such as the newt have remarkable regenerative ability, and a critical aspect of this is the ability of differentiated cells to re-enter the cell cycle and lose their differentiated characteristics. Unlike mammalian myotubes, cultured newt myotubes are able to enter and traverse S phase, following serum stimulation, by a pathway leading to phosphorylation of the retinoblastoma protein. The extracellular regulation of this pathway is unknown. RESULTS: Like their mammalian counterparts, newt myotubes were refractory to mitogenic growth factors such as the platelet-derived growth factor (PDGF), which act on their mononucleate precursor cells. Cultured newt myotubes were activated to enter S phase by purified thrombin in the presence of subthreshold amounts of serum. The activation proceeded by an indirect mechanism in which thrombin cleaved components in serum to generate a ligand that acted directly on the myotubes. The ligand was identified as a second activity present in preparations of crude thrombin and that was active after removal of all thrombin activity. It induced newt myotubes to enter S phase in serum-free medium, and it acted on myotubes but not on the mononucleate precursor cells. Cultured mouse myotubes were refractory to this indirect mechanism of S-phase re-entry. CONCLUSIONS: These results provide a link between reversal of differentiation and the acute events of wound healing. The urodele myotube responds to a ligand generated downstream of thrombin activation and re-enters the cell cycle. Although this ligand can be generated in mammalian sera, the mammalian myotube is unresponsive. These results provide a model at the cellular level for the difference in regenerative ability between urodeles and mammals.