Ehrenberg lab

Popular science presentation

The ribosome and its helping factors constitute the efficient machinery by which the cells construct all the proteins needed in life, both as simple unicellular organisms and as parts of complex multicellular organisms such as humans. The ribosomes are composed of two subunits, the small and the large subunit. The ribosomes link amino acids into long peptide chains, and the amino acid sequences determine the structures that the chains fold into, which in turn determine the function of the proteins in the cell.

The sequences of the peptide chains are coded in the genes in the DNA. In the process called transcription, RNA polymerase transcribe the information from the genes to messenger RNA (mRNA), which is positioned between the two subunits of the ribosome at the initiation of protein synthesis and read by the ribosome in order to construct a correct peptide chain.

Each amino acid is chemically associated with one or more transport RNAs (tRNAs). They arrive at the ribosome in complex with the helping protein EF-Tu and decode the mRNA so that the amino acids are inserted in the correct order in the peptide chain. When an amino acid is incorporated in the peptide chain, the mRNA and tRNA with the aid of the helping protein EF-G are moved, or translocated, backwards by one code word within the ribosome, so that a new tRNA with a new amino acid can enter the ribosome and be linked to the growing peptide chain. This continues until the peptide chain is finished, and released from the ribosome using two termination factors. The ribosome is then recycled by separation of the two subunits so that it may translate the next protein. Again, the factor EF-G assists, together with the ribosomal recycling factor (RRF).

In our research we study every step of this entire process, mainly for bacterial protein synthesis but also some translation factors from eukaryotes (the evolutionary group that includes humans). The transcription of mRNA from DNA is described by mathematical models, in order to understand how the RNA polymerase can synthesize mRNA with the very high precision that has been observed. The initiation of protein synthesis and the repeated elongation of the peptide chains are studied using methods of biochemistry. A great interest of our group is how accurately the tRNAs can decode the mRNA, how this accuracy is achieved and how it improves or worsens by mutations, antibiotics or the surrounding conditions.

We are also interested in how the other processes of protein synthesis, such as initiation, translocation, termination and recycling, can be so fast and accurate. Previously, these processes could only be studied by “freezing” the ribosomes of the desired conformation, but the frozen complexes do not correspond to the authentic, functional complexes in the kinetic progress of the ribosomal functions. One solution is cryo-electron microscopy, which we utilize in collaboration with Columbia University, NY, USA. In another collaboration, with the University of Hamburg, we use a method to detect the position of ribosome on the mRNA in order to study the effect of antibiotics on translocation and recycling. We also use mathematical models and stochastic simulations to study the effect control systems of gene expression of growing bacteria, and how the control systems are affected by antibiotics.

Research projects

Protein synthesis

The goal is to understand the mechanisms of termination of protein synthesis, recycling of ribosomes from termination back to initiation, initiation of protein synthesis, elongation of proteins, accuracy of tRNA and release factor selection by the messengerRNA coded ribosome, toxicity of mini-genes and drop-off of peptidyl-tRNA. We use quantitative biochemical methods in combination with molecular genetics and experiments on living bacteria. Future directions include studying mechanisms for protein export and structural analysis of important, functional ribosome-factor complexes.

Protein synthesis in biotechnology

The goal is to constitute an in vitro system for bacterial protein synthesis which can be used to (i) produce any conceivable protein in large scale starting from its gene sequence (ii) synthesise proteins which are isotope labelled in chosen regions to facilitate structural analysis with NMR (iii) develop new, powerful techniques for combinatorial design of oligo-peptides and proteins and apply these methods to obtain new antibiotics, new protein biosensors and new catalysts.

Systems Biology

The Ehrenberg lab is actively exploring a number of topics in the area of Systems Biology.

• Stochastic modelling of copy number control for plasmids, with special reference to plasmids ColE1 and R1. The focus has been on how plasmids can achieve precise control of copy numbers to minimize plasmid losses at cell division also when their average copy numbers per cell are small.
• General features of noise in intracellular control systems. This area includes hyper-fluctuations in intracellular chemical reactions which operate near criticality and a suggestion, stochastic focusing, for how noise can enhance, rather than reduce sensitivity in molecular control systems.
• Regulation of protein synthesis, adaptation and growth control in bacteria. This area deals with how bacteria with the help of local control systems for regulation of gene expression (e.g. repressors and attenuation of transcription) in combination with global control systems (e.g. the stringent response to amino acid starvation) can grow fast in different media and adapt rapidly to environmental changes. Theoretical modelling and experimental approaches are combined.
• Action of antibiotics and mechanisms for antibiotic resistance in bacteria (in collaboration with Tanel Tenson, Tartu). This work is primarily dealing with the action of macrolides on bacterial protein synthesis and descriptions of a number of resistance mechanisms against these drugs. Theoretical modelling and experimental approaches are combined.
• Development of numerical methods for stochastic descriptions of intracellular reaction-networks including diffusion-reaction couplings (in collaboration with Per Lötstedt, Scientific Computing, Uppsala University). This work is dealing with developments of efficient algorithms for numerical solutions of the master equation in intracellular chemical networks. It also concerns descriptions of diffusion-reaction couplings in macroscopically bistable systems.

In collaboration with

• Tanel Tenson, Tartu University, Estonia. Group leader
• Per Lötstedt, Uppsala University, Sweden. Group leader
• Otto Berg, Uppsala University, Sweden. Emeritus
• Hans Bremer, University of Dallas, Texas, USA. Emeritus
• Zoya Ignatova, University of Hamburg, Germany. Group leader