The nucleoid-associated protein IHF acts as a ‘transcriptional domainin’ protein coordinating the bacterial virulence traits with global transcription

Abstract

Bacterial pathogenic growth requires a swift coordination of pathogenicity function with various kinds of environmental stress encountered in the course of host infection. Among the factors critical for bacterial adaptation are changes of DNA topology and binding effects of nucleoid-associated proteins transducing the environmental signals to the chromosome and coordinating the global transcriptional response to stress. In this study, we use the model phytopathogen Dickeya dadantii to analyse the organisation of transcription by the nucleoid-associated heterodimeric protein IHF. We inactivated the IHFα subunit of IHF thus precluding the IHFαβ heterodimer formation and determined both phenotypic effects of ihfA mutation on D. dadantii virulence and the transcriptional response under various conditions of growth. We show that ihfA mutation reorganises the genomic expression by modulating the distribution of chromosomal DNA supercoils at different length scales, thus affecting many virulence genes involved in both symptomatic and asymptomatic phases of infection, including those required for pectin catabolism. Altogether, we propose that IHF heterodimer is a ‘transcriptional domainin’ protein, the lack of which impairs the spatiotemporal organisation of transcriptional stress-response domains harbouring various virulence traits, thus abrogating the pathogenicity of D. dadantii.

RNA chaperones Hfq and ProQ play a key role in the virulence of the plant pathogenic bacteriumDickeya dadantii

“…The hfq gene is part of the well conserved amiB-mutL-miaA-hfq-hflXKC cluster (Tsui and Winkler, 1994), while proQ is localized between yebR and prc . Inspection of the transcriptomes of D. dadantii under various physiological conditions (Reverchon et al, 2021) showed that transcription of hfq could be driven by (i) a promoter upstream of mutL , (ii) a promoter inside mutL and upstream of miaA , or (iii) two promoters inside miaA and upstream of hfq (Figure S2). Considering the expression level of mutL-miaA-hfq genes, it appears that hfq was largely transcribed from the two promoters inside miaA and rarely co-transcribed with miaA .…”

“…The copyright holder for this preprint this version posted March 26, 2021. ; https://doi.org/10.1101/2021.03.26.437193 doi: bioRxiv preprint Dickeya dadantii proQ and hfq mutant characterization (Reverchon et al, 2021) showed that transcription of hfq could be driven by (i) a promoter upstream of mutL, (ii) a promoter inside mutL and upstream of miaA, or (iii) two promoters inside miaA and upstream of hfq (Figure S2). Considering the expression level of mutL-miaA-hfq genes, it appears that hfq was largely transcribed from the two promoters inside miaA and rarely co-transcribed with miaA.…”

Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors

“…Additional relevant features of genomic spatial organization are manifest in the emergence of sub-chromosomal domains eliciting peculiar patterns of gene expression, denoted as coherent domains of transcription (CODOs) [110]. Under different growth conditions various constellations of CODOs were observed both in commensal E. coli [30] and in plant pathogen D. dadantii [16,111,112]. The CODOs harbor functionally linked genes, the coordinated expression of which is related to particular physicochemical and structural-dynamical properties of their encoding DNA sequences [16,30] and is distinctly impacted by DNA topology-modulating effects of the NAPs [16,111,112].…”

“…It is noteworthy that except IHF, all the NAPs examined here affect the global DNA topology by constraining DNA supercoils and stabilizing higher-order nucleoprotein structures, while IHF is apparently incapable of oligomerization. On binding DNA, IHF stabilizes planar bends rather than writhed coils [115] and affects local DNA trajectory, rather than global DNA topology [112,116]. The sequence-specificity of IHF binding is almost entirely determined by structural features of the DNA and not by direct readout of the base sequence [117], yet similar to the global TFs, IHF recognizes a relatively welldefined sequence motif [118] introducing sharp bends (U-turns) in the DNA.…”

“…The sequence-specificity of IHF binding is almost entirely determined by structural features of the DNA and not by direct readout of the base sequence [117], yet similar to the global TFs, IHF recognizes a relatively welldefined sequence motif [118] introducing sharp bends (U-turns) in the DNA. Stabilization of such tightly bent structures could explain, why IHF in contrast to other NAPs, is primarily affecting the directionality (leading/lagging strand bias) of genomic transcription with associated transcription-coupled supercoil diffusion [112]. Put another way, IHF exerts its primary effect at that level of genomic organization (mutual orientation of transcription units), for which the promoter sigma factor specificity is, most probably, immaterial.…”