Genetics, Epigenetics & Gene Regulation | Nucleus & Chromosome Biology | Structural & Computational Biology
Nuclear Envelope Biology - Gates, Chromatin & Lipids
The nuclear envelope is the signature of eukaryotes. Sculpted out of the endoplasmic reticulum by evolution, it serves as the protective vessel for the genome and as a highly regulated membrane barrier separating nucleus and cytoplasm. The nuclear envelope combines durability with plasticity - selective traffic with mass transport - spatial enclosure with sophisticated signaling. How this is achieved remains one of the biggest puzzles in cell biology...more
The nuclear envelope is the signature of eukaryotes. Sculpted out of the endoplasmic reticulum by evolution, it serves as the protective vessel for the genome and as a highly regulated membrane barrier separating nucleus and cytoplasm. The nuclear envelope combines durability with plasticity - selective traffic with mass transport - spatial enclosure with sophisticated signaling. How this is achieved remains one of the biggest puzzles in cell biology.
Our goal is to understand how the nuclear envelope enables cells to protect, decode and regulate the genome. A particular focus lies on the nuclear pore complexes (NPCs), nature’s largest proteinaceous channels. Like the gates of a fortified city, NPCs not only provide a point of controlled entry and departure, but are zones of communication and trade. In doing so, NPCs are fascinating examples of how different functions of the nuclear envelope are integrated in a single structure.
My group is interested in four main areas:
Adaptors at the Nuclear Pore
The function of NPCs in nucleocytoplasmic transport is well studied. However, NPCs carry out additional, unconventional duties. In particular, they impact on chromatin architecture and gene activity by physically interacting with the genome. A key question is how NPCs ‘communicate’ with the gene expression machinery. We recently discovered that the NPC basket employs dedicated Adaptors such as TREX-2 and Mediator to influence RNA Polymerase II activity (Schneider et al., Cell 2015). Specifically, a dedicated region of TREX-2 was found to interact with Mediator and to regulate both the assembly status of Mediator and the phosphorylation status of RNA Pol II. This study established a direct link between TREX-2 and Mediator and provided mechanistic insights into how NPCs participate in decoding the genome.
Lipid Metabolism of the Inner Nuclear Membrane
From a cytoplasmic view, the inner nuclear membrane is the most remote territory of the endoplasmic reticulum (ER), both in distance and difficulty of access. To get there, any lipid or protein must pass through the NPCs. Whereas the ER and outer nuclear membrane are highly active in converting nutrients into building blocks for lipids and membranes, the inner nuclear membrane was thought to be metabolically inactive and to receive its entire lipids from the ER via the NPC route. We recently discovered metabolic turnover of lipids at the inner nuclear membrane of budding yeast, and found that the inner nuclear membrane can form lipid droplets that are used for lipid storage (Romanauska & Köhler, Cell 2018). We identified the genetic circuit for the synthesis of nuclear lipid droplets and showed how these organelles participate in gene regulation. This study opens avenues for exploring how inner nuclear membrane lipids signal to the genome and which role the inner nuclear membrane plays in human metabolic diseases.
Animated 3D EM reconstruction of a lipid droplet-producing cell nucleus. Nuclear lipid droplets are colored in gold, the outer nuclear membrane is studded with ribosomes (red spheres). Inner nuclear membrane evaginations are putative sites of nuclear lipid droplet biogenesis. For further details see Romanauska & Köhler, Cell 2018.
Shaping the Nuclear Envelope
The assembly of new NPCs is tightly controlled. NPCs are embedded in holes formed by the fusion of the outer and inner nuclear membranes. Inserting a new NPC into an intact nuclear envelope is a fascinating, but poorly understood mechanical problem. Put simply, a hole must be pierced without the balloon popping. Specifically, the inner and outer nuclear membrane have to be bent and fused to open a pore membrane, which has to be stabilized afterwards. In conjunction with this membrane remodeling event, ∼500 nuclear pore proteins have to assemble into a functional NPC to prevent uncontrolled leakage of nuclear or cytoplasmic material. We have discovered a new function for the NPC basket in shaping the nuclear membrane to promote NPC and nuclear envelope integrity (Mészáros et al., Dev Cell, 2015). Future studies aim at understanding how various NPC proteins cooperate to sculpt their membrane environment. We use biochemical reconstitution as a tool to get key insights into what is minimally needed and how mechanisms emerge from component parts.
Nuclear Ubiquitin Signaling
Related to our interest in gene expression, we are studying the modification of chromatin by ubiquitin. When appended to histones, ubiquitin functions as an important epigenetic switch to regulate multiple steps of transcription. Histone H2B monoubiquitination is mediated by the E2 and E3 enzymes Rad6 and Bre1 (Gallego et al., PNAS 2016). Their activity is counteracted by a deubiquitinase of the SAGA complex (Köhler et al., Cell 2010). We are dissecting the structure and function of this intricate molecular machinery to understand its biology in health and disease. Recently, we have begun to study selected aspects of nuclear protein quality control and its links to nuclear envelope homeostasis.
Decrypting Cryptobiosis in Tardigrades
Tardigrades (also known as water bears or moss piglets) are one of the most resilient animals on our planet: they withstand conditions that would fatal to nearly all other life forms on earth. This includes temperatures from close to absolute zero to about 150°C, pressures six times greater than those found in the deepest ocean trenches, ionizing radiation at doses lethal for a human, and even the vacuum of outer space. Tardigrades can go without food or water for decades, only to rehydrate, forage, and reproduce. They survive this by falling into an enigmatic state called cryptobiosis (hidden life), in which they are neither dead nor alive. We are investigating selected aspects of Tardigrade biology with the support of the Swiss NOMIS Foundation (http://nomisfoundation.ch). We want to understand their outstanding robustness, specifically, how nuclear envelope architecture and function is preserved under extreme conditions.
Our lab combines a broad range of techniques and we value interdisciplinary collaborations. We perform bottom-up biochemical reconstitution of complex systems as well as structural, proteomic and lipidomic studies. We further use genetics as well as high-resolution and electron microscopy as complementary in vivo approaches.
September 2018 - we welcome Edvinas from Lithuania, a previous VBC summer school student, who now joins the lab for his master thesis. Edvinas will study the mechanism of nuclear pore insertion into the nuclear envelope.
September 2018 - Adrià from Spain joins the lab as a PhD student. Adrià aims to crack the secrets of the allmighty tardigrades.
August 2018 - Congratulations to Laura, who successfully defended her PhD thesis with the highest grade! The power of biochemistry is indeed amazing… Many thanks to her family (coming from Spain by car) for organizing an amazing after-thesis party. The jamón ibérico de bellota was spectacular.
August 2018 - Adrià and Alwin attended the 2018 Tardigrade Conference in Copenhagen. Many things to learn from tardigrade zoology to genomics and a very interesting microscopy workshop on marine tardigrades
June 2018 - After a series of extremely hot days, we picked the coldest and rainiest one for our 1st lab barbecue this summer. But this could not spoil the great mood! Not even the world-cup soccer game, in which Ina’s favorite team lost. As usual, vegan treats and soft drinks.
June 2018 - Ana from Portugal joins the lab for an internship. Welcome!
Anete’s paper is accepted in CELL. Congratulations! This calls for a proper celebration.
May 2018 - Anete presents her work at the Cold Spring Harbor Meeting on Nuclear Organization & Function.
May 2018 - The Ubiquitin symposium was a huge success.
Every year, members of the Vienna Biocenter Ubiquitin club make a great effort to organize the “Ubiquitin & Friends” symposium. Leading international scientists presented their latest discoveries and could intensively interact with students and postdocs. What is special about this event is the combination of outstanding science and the relaxed and collegial atmosphere.
January 2018 - Welcome Ina.
She joins the lab as a new PhD student to crack the secrets of the nuclear pore complex.
January 2018 - Fabio joins the lab as a technician.
He will strengthen the nuclear pore subgroup. Welcome!
Katharina joins us for an internship.
Thanks to everyone for an intense 2017 Lab Christmas Party! This marks the end of a successful scientific year.
ERC Consolidator Grant!
We just received our second ERC grant, which will be a strong support for our studies on the nuclear pore complex for the next 5 years.
Acknowledging Female Excellence
Laura and four other scientists were awarded the prestigious UNESCO-L’Oreal „For Women in Science“ scholarship. The award ceremony took place in the magnificent halls of Austrian Academy of Sciences. Claudie Haigneré, a former French astronaut, gave an inspiring talk about the importance of science and rationalism in world of volatility, uncertainty, complexity and ambiguity. Her advice for women: „Take risks. Take time. Take care.“
November 22nd 2017 - Ana Krolo has successfully defended her PhD Thesis
Congratulations from all of us!!! You did it.
Opening of our ‘Brain Room’
The ‘Brain Room’ was recently painted and equipped with a new sofa and guitar. This small room connects the two labs and is our creative space for scientific discussion and relaxation. The wall was decorated with a quote of the physicist Richard Feynman: "What I cannot create, I do not understand" –This is precisely our biochemical mission.
Laura selected as Medical University of Vienna ‘Researcher of the Month’
Laura was chosen for her outstanding scientific achievements and ranks among the best PhD and Postdoc scientists of the Medical University of Vienna. Congratulations! The award ceremony will take place on December 13th.
Vienna Biocenter Summer School 2017
Welcome Anamaria and Edvinas! Anamaria participates in this year’s summer school and Edvinas returns after being part of the 2016 summer school. The summer school is a unique opportunity for about 20 international undergraduate students to work on an exciting scientific project for 2 months and a perfect preparation for those who are interested in graduate studies. www.vbcphdprogramme.at/summer-school/
Ubiquitin 2017 Award for Laura - Congratulations!
Laura receives the “Ubiquitin Award” for her excellent talk during the recent "Ubiquitin and Friends" symposium. The prize is shared with Marcin Suskiewicz from Tim Clausen’s group at IMP. Both were selected by Rachel Klevit (USA) and Ami Navon (Israel), this year’s guest speakers and jury. This was the highly anticipated 4th annual "Ubiquitin and Friends" symposium, which is organized by VBC students and features distinguished international experts in the Ubiquitin field.
Lab retreat in the mountains
We just returned from our annual lab retreat in the Tatra mountains in Slowakia. Intense scientific discussions about our progress and future perspectives, hiking trips and evening barbecues made this a memorable and fun event. Thanks to Rado for organizing the trip, Stefan for coming a long way and Jakub for amazing skills on the Ukulele.
Jakub is selected to join the EMBO practical course on protein-lipid interactions in Helsinki, Finland. This hands-on course will teach cutting edge experimental and computational tools and fits perfectly with our interests on how nuclear pore proteins shape the nuclear envelope.
Romanauska, Anete; Köhler, Alwin (2018). The Inner Nuclear Membrane Is a Metabolically Active Territory that Generates Nuclear Lipid Droplets. CELL. PMID: 29937227
Gallego, Laura D; Ghodgaonkar Steger, Medini; Polyansky, Anton A; Schubert, Tobias; Zagrovic, Bojan; Zheng, Ning; Clausen, Tim; Herzog, Franz; Köhler, Alwin (2016). Structural mechanism for the recognition and ubiquitination of a single nucleosome residue by Rad6-Bre1. P NATL ACAD SCI USA;113(38):1055310558. PMID: 27601672
Schneider, Maren; Hellerschmied, Doris; Schubert, Tobias; Amlacher, Stefan; Vinayachandran, Vinesh; Reja, Rohit; Pugh, B Franklin; Clausen, Tim; Köhler, Alwin (2015). The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression. CELL;162(5):1016-28. PMID: 26317468
ERC Consolidator Grant 2017
Awardee of a "Consolidator Grant" from the European Research Council ERC!
Recipient of the NOMIS Pioneer Award
Start Prize 2011, Austrian Science Fund FWF
Project title: "The role of the nuclear pore complexes in gene regulation"
ERC Starting Grant 2011
Awardee of a "Starting Independent Researcher Grant" from the European Research Council ERC!
Austrian Academy of Sciences
DOC Fellowships for Laura Gallego and Jakub Cibulka