24.06.2024 2024 Summer Symposium on 12 July
At this year's Symposium in Marburg, GRK 2937 welcomes Prof. Iwona Mruk (Gdansk), Prof. Ben Luisi (Cambridge), Dr. Rebecca Hinrichs (Marburg), Dr. Georg Hochberg (MPI Marburg), Prof. Kristina Jonas (Stockholm) and Prof. Urs Jenal (Basel).
Registration and how to get there
We are looking forward to a great event and audience! Please click here to register by 4 July.
The Symposium will take place in the SYNMIKRO lecture hall and foyer. Click here for the directions to the Centre for Synthetic Microbiology, SYNMIKRO.
Programme
13:00 Welcome
13:05 Prof. Iwona Mruk Gdansk
Horizontal gene transfer – a driven domino effect in transcription factors' regulatory networks leading to Escherichia coli cell death
Prokaryotic genomes are highly plastic and can utilize horizontal gene transfer to counteract genetic pressure or to resist environmental changes. In addition, constant gene influx is selected by the host mechanisms to ensure preservation of its fitness and genetic identity. However, acquiring the genetic modules with regulatory potential, such as transcription factors (TFs), might be a challenge for cell, as TF needs to exert its unique function, but also fit well into the host genetic networks. It is also very likely, that an imported TF may seriously interfere with the existing host regulatory interconnectivity, which results in cell death.
Here, we show the impact of a small TF, a C regulatory protein dedicated to control a Type II restriction-modification (R-M) system on accepting host E. coli K-12 cells. The C protein binds its target site within R-M operon, but is also able to interact to several unrelated (off-target) DNA sites within its accepting host genome. We claim that C protein and possibly most of TFs may exert this promiscuous binding to some extent. In particular, C protein interaction to unrelated site within operon of the cryptic Rac prophage triggers a cascade of regulatory perturbations on global level leading to cell death. In this molecular event, several TFs drive a domino effect to dysregulate their regulons and genetic network globally.
We show the molecular basis of this process and how E. coli uses its high genetic plasticity to rewire its global network to minimize the adverse regulatory effects and to survive. This complex set of interactions may reflect the ability of bacteria to protect themselves by having robust mechanisms to maintain the integrity of their established regulatory networks.
14:00 Prof. Ben Luisi Cambridge
Dynamic ribonucleoprotein complexes in the control of bacterial gene expression
The lifetime of transcripts is a key aspect of the control of gene expression in all domains of life. In representative bacterial species, the turnover and processing of transcripts is mediated by multi-enzyme assemblies, referred to as the RNA degradosome. These machines can recruit small regulatory RNAs for targeted action on defined transcripts. RNA chaperones, such as the protein Hfq, play a key role in the post-transcriptional control of gene expression mediated by the degradosome. A model will be described proposing how Hfq works in conjunction with some regulatory RNAs to guide the degradosome for action on targeted transcripts and may help in early transcript surveillance. We describe the components and organisation of the Escherichia coli RNA degradosome, and present data supporting a model for a highly dynamic assembly that can act cooperatively with chaperones through allosteric conformational switching and clustering for RNA-mediated gene regulation.
14:55 Coffee break
15:15 Dr. Rebecca Hinrichs Marburg
YhaM, the protecting roadblock for the replisome?
A reliable response to DNA damage is essential for living organisms to survive1. The consequences of DNA damage range from reduced fitness to various diseases such as cancer.
Bacillus subtilis (B. subtilis) reacts to DNA damage by invoking the SOS response, which is controlled and directed by the protein RecA and the transcriptional repressor LexA. The regulation of the SOS response involves 63 genes in 26 operons that contain a characteristic sequence, known as “SOS-box” and act in a plethora of cellular processes like DNA repair, DNA replication, or cell division.
One of these operons that has not been sufficiently studied so far contains yhaO- sbcE yhaM.
YhaM (yhaM) has been characterized as a member of a family of 3’- exoribonucleases bearing hydrolytic ribonuclease activity. It is characterized by its unique composition and arrangement of domains. The protein consists of an N- terminal oligonucleotide domain (OB) and a C-terminal metal dependent phosphohydrolase domain (HD). The involvement of YhaM could be demonstrated for different pathways of RNA degradation but its specific function is not clear.
Here we introduce YhaM as a new member of bacterial SOS response machinery. Our structural characterization revealed the formation of a hexamer ring in which the individual monomers are assembled in a head-to-tail conformation. The hexamer interface is formed by the HD domain and the OB domains decorate the opening of the resulting pore. From the data we have collected in biochemical and in vivo experiments, we hypothesize that the OB domain acts as a scanner that can identify chromosomal locations for hydrolysis. Microscopy analyses revealed that YhaM co-localized together with RecA during DNA damage. This is especially evident when interstrand crosslinks are formed by addition of mitomycin C (MMC) and we observed that loss of yhaM in B. subtilis leads to a MMC sensitive phenotype. This suggests that YhaM has its site of action on DNA (rather than RNA). This is further corroborated by the finding that overproduction of YhaM in B. subtilis results in a replication block and highly condensed DNA. Therefore, we introduce YhaM as a new member of bacterial SOS response machinery, based on its structural and catalytic properties.
15:45 Dr. Georg Hochberg MPI Marburg
Resurrecting ancient proteins to understand the biochemical past and present
Cells are filled with an astonishing variety of molecular protein complexes, which are crucial for virtually every aspect of cellular function. They are the products of a billion-years long and often erratic evolutionary process that we are only now beginning to decipher. It is our group's my ambition to understand the evolutionary mechanisms that give rise to such molecular complexity, but also to reveal how functional innovations in individual protein complexes have changed the course of history for life on earth. To do this, we use ancestral sequence reconstruction combined with biochemical characterization of resurrected proteins. This approach uses a protein family sequence alignment, a phylogenetic tree inferred from the alignment, and a model of sequence evolution to make a probabilistic estimate of the sequences of long extinct proteins. Producing and characterizing these ancestral proteins in the lab then allows us to understand the biochemistry of the ancient past. In this talk I will give two examples of this work: the evolution of the carboxylase Rubisco and how it learned to cope better with oxygen, and some onegoing work on the evolution of flavin based electron bifurcation.
16:15 Prof. Kristina Jonas Stockholm
Lon-mediated proteolysis in bacterial development and stress adaptation
Intracellular proteolysis is a critical process in all cell types. In bacteria, it is executed by highly conserved ATP-dependent proteases that recognize, unfold and digest protein substrates. One example is the Lon protease that is highly conserved and has critical regulatory and protein quality control functions. In this talk, I will highlight my group’s recent and on-going research on the cellular roles of Lon and the mechanisms governing highly specific and precisely controlled Lon-mediated proteolysis.
By using quantitative proteomics approaches, my group has identified >150 novel putative Lon substrate proteins in the model bacterium Caulobacter crescentus. Biochemical and cell biological characterization of several of these Lon substrates, revealed critical roles of Lon in temporally controlling cell differentiation, cell cycle processes as well as the general stress response. Our quantitative proteomics approaches have also led to the discovery of LarA, a novel direct regulator of Lon. We identified LarA as a strong interactor of Lon and found that it allosterically activates Lon at the onset of proteotoxic stress, when the proteolysis demand is high. In our ongoing work, we have expanded our work on Lon to the opportunistic pathogen Pseudomonas aeruginosa, which possesses two Lon proteases, belonging to distinct Lon subfamilies. As in C. crescentus, we have conducted proteomics-based searches for substrates of each of these Lon proteases. We verified several proteins involved in swimming, swarming and twitching motility as specific substrates of the canonical Lon, while the other Lon-like protease appears be specialized in degrading proteins mediating antibiotic tolerance.
17:10 Coffee break
17:30 Prof. Urs Jenal Basel
Surface colonization of a human pathogen revisited
While commensal bacteria generally respect natural barriers of the human body, pathogens are able to breach epithelia, invade deeper tissue layers and cause life-threatening infections. Pseudomonas aeruginosa, an opportunistic human pathogen, is a leading cause of severe hospital-acquired pneumonia, with mortality rates as high as 50% in mechanically ventilated patients. Effective colonization and breaching of lung mucosa are hallmarks of P. aeruginosa pathogenesis. But how P. aeruginosa collectively and individually adapts to optimize adherence, virulence and dispersal is largely unclear. Our recent studies revealed both deterministic and stochastic mechanisms that generate functionally distinct bacterial subpopulations to balance P. aeruginosa growth and dispersal on surfaces. I will first review these latest findings and will then put them into a physiological context by demonstrating how they contribute to the colonization and breaching of human lung epithelia. Exposing the respective mechanistic details opens up new ways to control mucosal infections by a major human pathogen.
18:25 Get-together