Annual Report

The fertilization of an egg by sperm is the beginning of new life. In this process, the genetic information of both parents is united in the fertilized egg cell. Initially, the genetic information in the nucleus is inactive, and the first cell division is induced solely by maternal gene products. However, from the second cell division on, the newly combined genetic information must be accessed. Together with my team, I have investigated this particular process and discovered a „spark of life”, a genetic factor, that “awakens” the DNA.

How does cancer arise? How does the cellular composition of a tumor change its malignant characteristics? These questions are difficult to answer, yet crucial to understand cancer and find a cure. Together with my two research groups, I succeeded in developing a completely new diagnostic approach to get one step closer to this goal. By combining four modern methods, we have developed a very powerful technology to better understand the mechanisms of health and disease.

Transfer RNAs (tRNAs) specifically deliver amino acids to ribosomes during the translation of messenger RNA (mRNA) into proteins. The abundance of tRNAs therefore has a profound impact on cells. However, determining the amount of each tRNA species in cells was limited because of technical challenges. We overcame these limitations thanks to mim-tRNAseq, a method that can be used to quantify tRNAs in any organism and will help improve our understanding of tRNA regulation in health and disease.

The field of synthetic biology aims to assemble life-like systems from inanimate building blocks. Our goal is not only to observe and describe processes of life, but also to mimic them. A key characteristic of life is its ability to replicate its own macromolecular components. We have generated a new in vitro system that can regenerate some of its own DNA and protein building blocks.

Cells contact other cells via precise docking points. Cell migration and immune reactions require a finely tuned attachment and detachment process. Therefore, the contact sites consist of a whole machinery of proteins, in which talin plays a central role. Using cryo-electron microscopy, we were able to show how talin can assume an inactive spherical shape and is thus inaccessible to contact other proteins. These results help to understand the adhesion mechanism and also dysfunctions in disease processes.

The ability of cells to sense and respond to mechanical signals is central to numerous biological processes. How mechanical signals are processed in cells has remained unclear, because techniques to detect the extremely small molecular forces in cells were missing. We therefore developed a technology that allows quantification of intracellular forces that are as low as a billionth of a newton. First applications reveal fascinating insights into the molecular mechanisms underlying cellular mechanobiology.

Reactive oxygen species (ROS) are commonly generated during virus infections, but their significance is only partially understood. We identified a cell death pathway, oxeiptosis, regulating cell death and cell survival after exposure to ROS. Manipulation of oxeiptosis impairs ROS - and virus - induced cell death in vitro and causes lung inflammation and tissue injury in influenza A infected mice. Since ROS are commonly generated during physiologic and pathologic situations, we anticipate that oxeiptosis plays a prominent role in attenuating a wide range of diseases.

Haploid gametes are produced in meiosis, a special form of cell division where DNA replication is followed by two rounds of chromosome segregation and gametogenesis. Homologous chromosomes segregate in meiosis I, whereas chromatids disjoin in meiosis II. Scientists of the research group Chromosome Biology now revealed how the conserved Hrr25 kinase of yeast coordinates production and packaging into gametes of the single-copy genome in meiosis II.

Faithful distribution of the genetic material during cell division relies on the folding of DNA into discrete and compact bodies called chromatids. SMC protein complexes have evolved to deal with the tangly nature of long DNA molecules. They act as molecular clamps that bring together selected DNA segments. The researchers determined the architecture of the ancestral SMC complex and elucidated its dynamic localization on the bacterial chromosome. The results indicate that SMC rings are not merely DNA linkers but active machines, which step-by-step enlarge DNA loops to organize chromosomes.

Autophagy is a recycling system of the cell that prevents all kinds of cellular waste from accumulating. Autophagy sequesters such material in specialized containers, which are like other organelles of the cell surrounded by a flexible membrane. These containers transport their contents to cellular recycling stations for degradation. The researchers recently identified a specialized set of proteins that stabilize autophagic containers. Similar to recycling bins, these proteins form a stiff shell on top of the membrane to provide physical support.

In spite of the great progress of the biosciences during the last decades, the very line of division between the animate and inanimate world still remains elusive. One of the most distinctive features of living systems is their compositional and organizational complexity, but how complex does life really have to be? Our research aims to identify a minimal set of fundamental features and governing principles of biological cells - being the smallest units of life - to enable their comprehensive biophysical, i.e., quantitative characterization by a defined set of parameters.

The cilium is a slim hair-like structure found on almost all cells in our body. The cilium functions both in motility and as an antenna that allows sensation between cells and the environment. To build a functional cilium, the cell relies on intraflagellar transport (IFT). A failure to complete the process of IFT leads to human diseases including infertility, blindness, mental retardation and cysts formation. How the cilium is formed and what goes wrong in cilium-related diseases is poorly understood and is the topic of intense research also because of its medicinal aspects.

When chromosomes mis-segregate during cell division, cells lose their balance. The resulting cells are aneuploid, they contain fewer or more chromosomes than usual. Aneuploidy is generally harmful for the cell and characteristic for pathological conditions such as Down syndrome or cancer. Scientists are currently investigating why aneuploidy is so harmful. Presumably, an imbalance of proteins present in aneuploid cells plays an important role in the process. Nevertheless, many questions regarding the origin of aneuploidy and its consequences still remain unanswered.

Proteins are synthesized as chains of amino acids. In order to fulfill a wide variety of biological functions, these chains must fold into specific three-dimensional patterns. This process of protein folding is mediated in our cells by molecular chaperones, helper molecules which act to prevent the clumping of faulty protein chains into aggregates. The formation of aggregates is the cause of neurodegenerative disorders, including Alzheimer’s and Parkinson’s disease. Understanding the role of molecular chaperones will help in developing treatments for these and other diseases.

Flying insects face the challenge to be up in the air. To stay airborne they need to oscillate their wings at frequencies up to 1000 times per second. These fast oscillations are powered by specialized flight muscles that contain a particular fibrillar organisation of their contractile apparatus and hence differ from all other muscles. In vinegar flies (Drosophila) the researchers identified a developmental switch gene, spalt, which induces the formation of these specialised flight muscles. Spalt mutants are flightless: their flight muscles have lost all their special properties.

Much in the same way as we use shredders to destroy documents that are no longer useful or that contain potentially damaging information, cells use molecular machines to degrade unwanted or defective macromolecules. A key player in the degradation of RNAs is the exosome complex. Our work has revealed how the exosome binds and shreds RNAs by a channeling mechanism that is largely conserved in all kingdoms of life and that parallels the mechanism used by the proteasome to degrade polypeptides.

Our bodies are constantly under attack by hostile microorganisms, such as bacteria and viruses. Immune cells can identify foreign microbial components through a host of cell surface receptors. These receptors relay signals to the nucleus, where transcription factors activate the expression of genes whose protein products help fight the invaders. Misguidance of immune mechanisms can result in autoimmunity and leukemias or lymphomas. Researchers employ genetic mouse models to understand how signal transduction orchestrates immune responses and how its deregulation causes disease.

Modification of proteins can alter their function. If proteins are modified by the small protein ubiquitin, the proteins are usually targeted for degradation. However, our work has shown that ubiquitin and its related protein SUMO can also mediate DNA repair and genome stability. In human, this mechanism is important to avoid tumor formation.

Cranes, dump trucks, power shovels and lots and lots of workers: The tight organization of large construction sites reveals itself only to the patient observer. Similar endurance is needed when scientists study cellular processes. With the help of new microscopes, sensitive cameras and computational approaches cell biologists reveal new types of structures and processes and analyze them with nearly mathematical precision. Step by step a new image of the cell emerges – as a highly dynamic and strictly coordinated biological system.

The genes of an organism are only the blueprint for the real functional entities of the cell - the proteins. So far it was unfortunately not possible to analyse proteins with the same accuracy and depth as the genetic material, the DNA. Scientists at the Max-Planck Institute of Biochemistry have now measured the totality of all proteins of an organism – its proteome – for the first time. Possible applications of this technology include almost all areas of basic biology and may include cancer diagnosis in the future.

The genetic information encoded by DNA is transcribed to mRNA molecules which are subsequently translated into proteins. However, only a minor portion of the human genome encodes for proteins. The bulk of the human DNA is non-coding. Interestingly, non-coding DNA is constantly transcribed into non-coding RNA and it was found that such non-coding RNAs have fundamental cellular functions. Extensive research of the past years revealed that non-coding RNAs can also play important roles in the pathogenesis of diseases including various forms of cancer.

Semiconductor chips and neuronal systems can be electrically coupled on a microscopic level. This research provides the fundament for an application of such hybrid processors in brain research, neuroprosthetics and information technology. On the neuronal side, ion channels, nerve cells and brain tissue are employed. On the electronic side, simple silicon chips with transistors and capacitors are used for the elucidation of the coupling mechanism. On that basis, complex chips are developed with more that 30000 contact sites to supervise neuronal activity with highest spatial resolution.

The structure of viruses provides a remarkable example of simplicity and functionality in biological systems. Composed of a limited number of proteins and often organized according to geometric principles, viral particles are effective devices in the transfer of the viral genome and proteins to host cells. To determine the molecular interactions, cryo electron tomography is employed to reveal the molecular players through which viruses communicate with their hosts and to understand how viruses take advantage of cellular cues in infection and for replicating themselves efficiently.

This article describes an optical microscopy method with nanoscale resolution independent of the wavelength, based on atomic force microscopy, where a scanning tip is used for mechanical probing and for scattering optical near-fields. Operating at infrared frequencies, potential applications range from characterization of solid state surfaces to identification of single nanoparticles and macromolecules.

Life in concentrated brines under extreme conditions of nutrition requires extreme adaptation. By molecular and functional analysis of cellular constituents of halophilic archaea it is possible to gain insight into the biology of these fascinating organisms on a systems level of the cell.

The exact halfing of the previously replicated chromosomes during mitosis and both meiotic divisions is crucial to avoid tumor formation and trisomies. Chromosomes are separated by action of separase, a giant protease, which cleaves chromosomal cohesin. Researchers from the Max-Planck-Institute of Biochemistry recently discovered a new regulation and an unexpected, non-proteolytic function of this key enzyme.

Our research focuses on the regulation of substrate specificity in the ubiquitin proteasome system, specifically on two modular protein complexes: the CBC^VHL ubiquitin ligase with its substrate binding subunit, the von-Hippel-Lindau tumor suppressor protein, and the chaperone-like Cdc48 AAA ATPase with cofactors of the UBX protein family. UBX proteins bind to Cdc48 and thereby regulate the specificity of Cdc48 activity in various cellular processes. UBX proteins with a ubiquitin binding UBA domain recruit ubiquitylated substrates which are targeted via Cdc48 for proteasomal degradation. One such UBA/UBX protein, called Ubx2, plays a central role in endoplasmic reticulum (ER) associated protein degradation (ERAD). Biochemical studies of tumor associated mutants of the von-Hippel-Lindau tumor suppressor protein provide new insights in the complex genotype/phenotype relationship of the von-Hippel-Lindau disease. For instance, the extent of functional defects on the molecular level correlates with the patients´ risk of developing renal cell carcinomas.

Coordinated growth and differentiation of specialized tissues during the development of higher eukaryotes requires precisely regulated communication between the multiple cell types of an organism. The same holds for the maintenance of all life functions of mature organisms. Defects in the cellular communication network cause multitudes of pathological phenomena such as cancer, diabetes and neurodegenerative diseases. The research program of the Department of Molecular Biology is focussed on the elucidation of such critical biological and pathophysiological processes. Main emphasis of the research efforts is on the investigation of signaling mechanisms in normal cells and degeneration of signaling pathways in cancer.

Our department is involved in the development and application of new microscopical methods. The automated cryo-electron tomography images ice-embedded macromolecular complexes, viruses, prokaryotes, and eukaryotic cells in a native state and yields 3D-reconstructions at molecular resolution. The technique offers the perspective to analyse the interactions of macromolecular complexes in individual cells in a near-to-live state. Infrared near-field microscopy enables high-resolution topographic imaging of, e.g., organic materials or single viruses together with simultaneous recording of local infrared absorption.

The aim of our group is to understand the function and regulation of the transcription factors p53 and c-MYC, as well as the processes and genes which they regulate. c-MYC and p53 are genes which are altered in more than 50% of all cancers. The tumorsuppressor gene product p53 is activated after DNA damage and induces genes, as 14-3-3sigma, which mediate cell cycle inhibition. p53 is an integral part of the program of cellular senescence. In contrast, activation of the c-MYC oncogene leads to immortalization. How this function of c-MYC is achieved is a focus of our studies. In addition, we are identifying and characterizing genetic and epigenetic alterations which contribute to prostate cancer and malignant melanoma. For these projects we are using novel proteomic and genomic approaches.

We investigate integrin-mediated adhesion in various tissues of mice. To this end we establish mouse models with targeted mutations in extracellular matrix proteins, integrins and integrin-associated proteins. The consequence of the mutations are analyzed during mouse development, which allows to assess the physiological function of the mutant gene, and disease situations such as inflammation tissue repair and tumor formation.

Animal cell growth and division requires the constant delivery of new proteins and lipids from their site of synthesis in the endoplasmic reticulum to the cell surface. Cell growth and DNA replication in S-phase is followed in M-phase by the ordered segregation of the genetic material into two equivalent sets of chromosomes, then by a cleavage event termed cytokinesis which divides the cell into two such that each part contains one complete set of genetic material (Figure 1). Investigation of these processes and their regulation at a molecular level is therefore important for understanding both normal cell growth and division and how, when cell division fails, the aneuploid cells that contribute to human tumour formation arise. My group is interested in understanding how human cells establish and regulate the complex three-dimensional structures necessary for cell growth and division. To do this we have focussed our work on two areas central to these processes: (i) protein traffic and the function of the key organelle of the secretory pathway, the Golgi apparatus; and (ii) the function of the central spindle in protein trafficking events that lead to cytokinesis.