Essential Nucleoid Associated Protein mIHF (Rv1388) Controls Virulence and Housekeeping Genes in Mycobacterium tuberculosis

Abstract

Tight control of gene expression is crucial for Mycobacterium tuberculosis to adapt to the changing environments encountered when infecting or exiting human cells. While three nucleoid associated proteins (NAPs) EspR, HupB and Lsr2 have been investigated, the role of a fourth, the mycobacterial integration host factor (mIHF), remains elusive. Here, we report a multidisciplinary functional analysis that exploits a conditional mIHF mutant. Gene silencing was bactericidal and resulted in elongated cells devoid of septa, with only one nucleoid. ChIP-sequencing identified 153 broad peaks distributed around the chromosome, which were often situated upstream of transcriptional start sites where EspR also bound. RNA-sequencing showed expression of 209 genes to be heavily affected upon mIHF depletion, including those for many tRNAs, DNA synthesis and virulence pathways. Consistent with NAP function, mIHF acts as a global regulator by directly and indirectly controlling genes required for pathogenesis and for housekeeping functions.

Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening

“…4a – d ). mIHF is one of the four mycobacterial nucleoid associated proteins (NAPs) that impact the expression of hundreds of genes by shaping chromatin architecture, and thus directly and indirectly controlling genes required for pathogenesis and for housekeeping functions 34 . The same peptide was tested in a previous report using ELISPOT analysis but did not yield a positive readout according to IEDB ( http://www.iedb.org ).…”

Nucleoid Associated Proteins: The Small Organizers That Help to Cope With Stress

“…These small basic proteins shape chromosomal DNA, adjusting its architecture in response to intra-and extracellular conditions. When the bacterial cell detects strong stress, NAPs (e.g., HU, Dps) generally coat and/or condense the nucleoid, creating a physical protective barrier for the DNA (Nguyen et al, 2009;Salerno et al, 2009;Pandey et al, 2014;Crosby et al, 2016;Odermatt et al, 2018). More specific NAP-related stress response mechanisms involve the ability of NAPs to regulate transcription.…”

“…They all possess dimerization/oligomerization domains that facilitate chromosome coating and binding within the chromosomal regions to create inflexible filaments. Most NAPs show rather low sequence specificity for binding; however, their binding sites are often AT-rich, which is a characteristic feature of gene promoters (Kahramanoglou et al, 2011;Prieto et al, 2012;Odermatt et al, 2018). All bacterial species possess NAPs, some of which are unique for a given genus and/or species (Datta et al, 2019;Gehrke et al, 2019;Liu et al, 2019).…”

“…Both proteins exhibit a preference for AT-rich regions, but unlike HU, the IHF protein specifically recognizes 13-bp sequences with the consensus 5'-WATCAANNNNTTR-3' (Hales et al, 1994;Prieto et al, 2012). M. tuberculosis possesses homologs of both HU and IHF (HupB and mIHF, respectively), and these proteins are essential during the infection of macrophages (Pandey et al, 2014;Odermatt et al, 2018). Moreover, it was shown that expression of hupB gene increases during the infection (Kumar et al, 2011).…”

“…The mycobacterial HupB protein regulates the expression of the katG gene (acting as a repressor), whose product activates the anti-tuberculosis drug, isoniazid (Niki et al, 2012;Enany et al, 2017); a M. smegmatis strain deprived of HupB showed increased susceptibility to this drug (Hołówka et al, 2017). Additionally, recent studies showed that the M. tuberculosis mIHF protein represses the expression of many genes, including those connected with pathogenesis (Odermatt et al, 2018).…”