Functional Characterization of Nucleoid Associated Proteins Acting as Global Transcription Factors in Mycobacterium tuberculosis

The fatal lung disease tuberculosis is caused by the airborne Mycobacterium tuberculosis, a versatile pathogen adapted to rapidly changing environments. Instead of being eradicated by phagocytic cells of its human host, bacilli tune macrophages to support their own growth and even mask their presence from the immune system for several decades. Rapid adjustment of gene expression is critical for bacterial survival and heavily relies on nucleoid-associated proteins (NAPs). NAPs contribute to active DNA management by altering the chromosomal topology through bending, bridging and looping the DNA. These conformational changes can bring distant genetic loci into close spatial proximity or influence DNA supercoiling and therefore accessibility of the transcription machinery. Apart from their architectural role, NAPs moreover act as global transcription factors by direct regulation of numerous genes. In M. tuberculosis, five proteins were assigned a role as NAP. Among these, EspR, HupB and Lsr2 are crucial not only for virulence but also for cellular metabolism. This thesis focuses on the NAPs mIHF and H-NS with the objective of determining their function and target regulon. Both proteins were investigated by means of genetic manipulation, phenotype assessment and structural studies, and the efficiency of a potential new anti-tuberculosis drug acting on Lsr2 was assessed. Chrysomycin, described as specific inhibitor of Lsr2-DNA complex formation, was found to intercalate into the DNA. The resulting toxic effect on both its target M. tuberculosis as well as on eukaryotic cells rendered further development of the compound as an anti-tuberculosis drug futile. We demonstrated that Rv3852, formerly annotated as H-NS, does not act as a NAP. Deletion of the rv3852 gene had no effect on the in vitro phenotype of M. tuberculosis, did not alter nucleoid spread nor position and had no influence on virulence in mice. The mIHF protein on the other hand is not only essential for active bacterial growth, but also indispensable for survival. Generation of a conditional knockdown mutant showed that depletion of mIHF led to elongated cells devoid of septa with abnormal DNA localization and finally to cell death. The target regulon of mIHF was thoroughly studied by mapping its binding sites on the bacterial genome and by identifying genes that were differentially expressed upon depletion of the protein. We found that mIHF has a strong effect on virulence gene expression and, similar to EspR, possesses a major binding site upstream of one of the main virulence factor operons espACD. Analysis of the transcriptional response revealed that mIHF is further involved in the bacterial response to the host’s immune system, including control of nutrient pathways as well as global protein and nucleic acid synthesis. To define how mIHF interacts with DNA and influences its 3D organisation, the protein structure of mIHF was determined by nuclear magnetic resonance spectroscopy. Binding of mIHF introduced left-hand loops into linear as well as supercoiled DNA substrates, therefore unwinding condensed DNA. We identified two DNA binding domains in mIHF and showed that its stability increased substantially upon DNA binding. All together, the findings of this thesis contribute to a better understanding of the complex gene regulatory network of M. tuberculosis, advancing the knowledge necessary to eventually defeat tuberculosis, a disease that has plagued humanity for millennia.