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Scientists from Heidelberg study the assembly of ribosomes

Ribosomes are highly complex cellular nano-machines that synthesize new proteins. Their structure is relatively well known. They are assembled from immature pre-ribosomes in the cell nucleus in a process that involves numerous biogenesis factors. Researchers from Heidelberg have made a major contribution to our present understanding of the structure and function of the pre-ribosomal assembly and transport processes, and the biogenesis factors involved.

A typical liver cell weighs only around two billionths of a gramme (2 ng) and contains around 10,000 different proteins in varying quantities: around two thousand molecules of the proteins that occur in lower quantities, and up to several billion copies of the actin protein, which is the structural protein that forms microfilaments. These proteins are constantly being degraded and need to be replaced. They are synthesized in a process that translates the information contained in the nucleotide sequence of the mRNA into amino acid sequences. During translation amino acids are linked together to form a polypeptide chain which will later be folded into a protein. This process involves a complex nano-machinery consisting of ribosomes, messenger RNA (mRNA), transfer RNAs (tRNAs) and a number of different protein factors.

Highly effective nano-machines

Three-dimensional ribosome model. © DESY

The translation of mRNA into amino acids takes place at the ribosomes, i.e. aggregations of long ribosomal RNA chains (RNAs) and numerous ribosomal proteins (r proteins). The ribosomes synthesize proteins by joining amino acids attached to transfer RNA (tRNA) into a long polypeptide chain. The ribosomes move along the mRNA, reading the sequence and producing a corresponding chain of amino acids.

Several ribosomes simultaneously move along a given mRNA chain with  incredible efficiency: each ribosome joins around 15 amino acids per second. A liver cell contains ten million or more active ribosomes. The three-dimensional structure of ribosomes was clarified in detail by the American Thomas A. Steitz, the Indian Venkatraman Ramakrishnan and the Israeli Ada Yonath, who were jointly awarded the Nobel Prize in Chemistry in 2009 for “studies of the structure and function of the ribosome” (see Nobel Lecture given by Ada Yonath).

Thanks to the X-ray structure analyses that Ada Yonath, then head of a Max Planck Research Group at the Hamburg-based DESY, carried out with researchers from the European Molecular Biology Laboratory (EMBL), the structure-function relationships of the ribosomal binding sites and the individual protein biosynthesis steps are far better known than those of any other complex cell components. Research tools have since become available that can be used to investigate functional defects of ribosomes on the molecular and atomic level. There is an ever increasing number of diseases associated with ribosome malfunction, including severe metabolic disorders and diseases such as cancer.

The assembly of ribosomes

Prof. Dr. Ed C. Hurt © BZH Universität Heidelberg

An intensively studied issue and one that is of particular interest for nanobiotechnologists relates to the assembly of these highly efficient and complex cellular nano-machines: how are the individual ribosomal components formed and assembled into functional ribosomes? How are they transported to the site where they synthesize proteins? The assembly of ribosomes is the major research focus of Professor Dr. Eduard C. Hurt from the Biochemistry Centre at Universität Heidelberg (BZH).

Ribosomes consist of two subunits, a large one and a small one. The cytoplasmic ribosomes of eukaryotic cells are larger and more complex than prokaryotic ribosomes (the ribosomes of the mitochondria and chloroplasts of eukaryotic cells are also counted as prokaryotic ones). The two subunits of eukaryotic ribosomes, we will look at in this article, consist of two long and two short rRNA chains, which make up around two thirds of the entire ribosome mass, and more than 70 different r proteins.

Electron microscope image of the transcription of rRNA taking place in the nucleolus of a yeast cell. Explanation in the text. © Prof. Dr. M. Trendelenburg

The genes from which the rRNA chains are transcribed are located in one of several special chromosome regions (nucleoli, sg: nucleolus) in the cell nucleus. Cells with a high protein synthesis rate contain multiple repeated rRNA gene copies. The amplification of the rRNA genes makes it possible to visualize the process and components of rRNA biosynthesis under the electron microscope using a special spreading technique: the RNA-synthesizing enzyme complexes (DNA-dependent RNA polymerases) are arranged on a central rDNA thread at a distance of around 40 nm from each other. The RNA threads grow in length like twigs on trees. The first polymerase will already have “read” the entire gene when the last enzyme is only just starting the synthesis.

Assembly of pre-ribosomes in the cell nucleus

The assembly of the ribosomes from individual components starts in the nucleolus. In addition to four rRNA chains, 70 r proteins, ribosome construction involves around 200 pre-ribosomal helper proteins. These biogenesis factors are evolutionarily conserved. The pre-ribosomes function like an assembly line and have to go through a number of closely coordinated temporal and spatial steps before the matured ribosomal subunits leave the cell nucleus on their way to the cytoplasm. They bind to the evolving pre-ribosomes and act on them. These biogenesis factors are later withdrawn to enable the assembled ribosome to go about its work. The subunits are transported through pore complexes of the nuclear envelope. The nuclear pore complexes (NPC) are also complex nano-machines. They are composed of about 30 different components called nucleoporins (Nups), which have many copies, meaning that several hundred subunits build up this complex nano-machine. Nuclear pore complexes are one of Hurt’s major research areas (see: In vitro modeling of the nuclear pore complex of a thermophilic fungus).

Pre-ribosome (blue) with bound Rea1 ATPase (pink). The Rea1ATPase consists of a motor head and a long mobile tail. The motor head uses ATP to produce a vectorial force which releases biogenesis factors (green and yellow) from the pre-ribosomal particles via the tail. © Universität Heidelberg

Hurt’s group of researchers use the thermophile fungus Chaetomium thermophilum as a model organism for their investigations. In cooperation with a group of researchers led by Peer Bork at the European Molecular Biology Laboratory (EMBL), Hurt’s team sequenced the genome of this fungus, which consists of 28 million base pairs, and identified all the proteins of the nuclear pore transport channel. Ed Hurt was head of a research group at EMBL until 1995 when he was appointed professor at Universität Heidelberg. He has received numerous prizes for his achievement, including the Leibniz Prize, one of the most prestigious German science prizes, in 2001, and the Feldberg Prize for Anglo-German Scientific Exchange in 2007. His latest research project on the assembly of ribosomes runs until 2016 and is being funded with around 1.5 million euros by the German Research Foundation as part of a Reinhard Koselleck project.

Hurt explains that insights into the structure and function of the individual assembly tools and the rather complex assembly machinery in Chaetomium is also of great importance for medical applications. The ribosomes determine the rate of protein biosynthesis and the growth of cells. Therefore, errors occurring during the assembly and in the structure of ribosomes have been associated with diseases such as cancer. The biogenesis factors are therefore attractive targets for the treatment of cancer (see Heidelberger Biochemiker wird mit Reinhart-Koselleck-Projekt gefördert; only available in German).

A mechano-chemical tool

The ribosome can only exert its function when the biogenesis factors have been removed. Working with Dr. Bettina Böttcher (previously at EMBL, now at the University of Edinburgh, Scotland), Ed Hurt and his colleagues have identified the function of a mechanoenzyme involved in ribosome formation, namely the removal of the biogenesis factors from the pre-ribosome. This cellular tool is a motor protein with the name Rea1 ATPase, which converts the chemical energy arising from the hydrolysis of ATP into mechanical energy. The ATPase consists of a motor head and a long flexible tail, which dock to different sections on the pre-ribosome. The hydrolysis of ATP (energy generation) in the motor head leads to the build up of a tensile force. This force can be compared to a spiral spring and is transmitted to the ribosome precursor via the tail. The force ultimately ends up releasing biogenesis factors from the pre-ribosomal particles.

The clarification of the Rea1 ATPase mechanism is another important step on the way to understanding molecular mechanisms behind the biogenesis and function of ribosomes, those wonderful cellular nano-machines, which are much more complex than the construction plans human nanotechnologists are currently able to design.

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