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

Nina T Odermatt,Stewart T Cole,Claudia Sala,Andrej Benjak

doi:10.1038/s41598-018-32340-2

Nina T Odermatt, Stewart T Cole + Show 2 more

Open Access

https://doi.org/10.1038/s41598-018-32340-2

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Journal: Scientific Reports	Publication Date: Sep 21, 2018
Citations: 20	License type: open-access

Affiliation: École Polytechnique Fédérale de Lausanne

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.

Highlights

Discovered as being essential for mycobacterial phage L5 integration into the M. smegmatis genome[9], mycobacterial integration host factor (mIHF) was named after the E. coli counterpart, despite the two genes and their respective proteins showing no sequence similarity. mIHF is highly conserved among the Mycobacterium genus and even M. leprae, with its reduced genome, possesses a copy of mihF10, and orthologs occur in many other Actinobacteria
While some nucleoid associated proteins (NAPs) are present throughout the entire growth cycle of a bacterium, others peak at certain stages
The mIHF protein was identified at approximately 12 kDa by immunoblotting and a time-course analysis of protein levels showed that it is constantly present from the exponential to stationary phase with little fluctuations (Fig. 1a)

Summary

Introduction

Discovered as being essential for mycobacterial phage L5 integration into the M. smegmatis genome[9], mIHF was named after the E. coli counterpart, despite the two genes and their respective proteins showing no sequence similarity. mIHF is highly conserved among the Mycobacterium genus and even M. leprae, with its reduced genome, possesses a copy of mihF10, and orthologs occur in many other Actinobacteria. Discovered as being essential for mycobacterial phage L5 integration into the M. smegmatis genome[9], mIHF was named after the E. coli counterpart, despite the two genes and their respective proteins showing no sequence similarity. The mihF (rv1388) gene in M. tuberculosis was initially predicted to be 573 bp-long and to encode a ~20 kDa protein[11]. The mihF gene was predicted to be essential for in vitro growth with glycerol or cholesterol as carbon sources by Himar-1 based transposon mutagenesis[16], suggesting an important regulatory role in M. tuberculosis metabolism. The effect of mIHF depletion was investigated using ChIP-seq and RNA-sequencing thereby demonstrating that this NAP impacts M. tuberculosis gene regulation pleiotropically by controlling expression of housekeeping as well as virulence genes

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Conclusion