The HU Regulon Is Composed of Genes Responding to Anaerobiosis, Acid Stress, High Osmolarity and SOS Induction

Abstract

BackgroundThe Escherichia coli heterodimeric HU protein is a small DNA-bending protein associated with the bacterial nucleoid. It can introduce negative supercoils into closed circular DNA in the presence of topoisomerase I. Cells lacking HU grow very poorly and display many phenotypes.Methodology/Principal FindingsWe analyzed the transcription profile of every Escherichia coli gene in the absence of one or both HU subunits. This genome-wide in silico transcriptomic approach, performed in parallel with in vivo genetic experimentation, defined the HU regulon. This large regulon, which comprises 8% of the genome, is composed of four biologically relevant gene classes whose regulation responds to anaerobiosis, acid stress, high osmolarity, and SOS induction.Conclusions/SignificanceThe regulation a large number of genes encoding enzymes involved in energy metabolism and catabolism pathways by HU explains the highly pleiotropic phenotype of HU-deficient cells. The uniform chromosomal distribution of the many operons regulated by HU strongly suggests that the transcriptional and nucleoid architectural functions of HU constitute two aspects of a unique protein-DNA interaction mechanism.

The nucleoid-associated protein HUβ affects global gene expression in Porphyromonas gingivalis

“…We found that even in the absence of appropriate transcriptional inducer (IPTG) there was ample PG0121 protein expressed as shown by Western analysis (Fig. 1a, lane 5).It has been shown previously that an HU deficiency makes E. coli vulnerable to acidic conditions, resulting in a loss of viability (Bi et al, 2009;Oberto et al, 2009); therefore in our first complementation test, the HU-deficient HU (both HUa and HUb absent) was tested for low-pH sensitivity.As shown in Fig. 1(b), it is clear that while the double mutant is more susceptible to low pH than the wild-type parent strain, the PG0121-complemented strain restores acid resistance.…”

“…Plasmids were constructed in E. coli DH5a or BL21DE3 and then electroporated into P. gingivalis strain W83 using previously described methods (AlbertiSegui et al, 2010;Davey & Duncan, 2006). P1 transduction, using hup alleles provided by Oberto et al (2009), was performed as described by Thomason et al (2007) to isolate the various hup mutants. E. coli strains were grown in Luria-Bertani broth (LB) and maintained on LB containing 1.5 % w/v agar (LB agar) at 37 uC.…”

“…In Escherichia coli, HU proteins are differentially expressed during different phases of growth (Ali Azam et al, 1999) and recently it has been determined that this is also true for the bacterium Legionella pneumophila (Morash et al, 2009). With regard to function, HU has been shown to compact and prevent denaturation of DNA under detrimental conditions (Drlica & Rouviere-Yaniv, 1987;Oberto et al, 2009;Swinger & Rice, 2004) and to be involved in changing DNA topology (Swinger & Rice, 2004), specifically introducing negative supercoiling into relaxed DNA in the presence of topoisomerase I, in vitro (Bensaid et al, 1996). HU typically acts as an accessory protein in virtually all types of nucleoprotein-mediated processes (reviewed by Drlica & RouviereYaniv, 1987;Grove, 2011); such as acting as a cofactor to either stimulate or repress transcription (Aki et al, 1996;Morales et al, 2002) or aiding in translation (Balandina et al, 2001).…”

“…Strains with mutations in both the a and b-subunits have increased sensitivity to UV and ionizing radiation (Boubrik & Rouviere-Yaniv, 1995;Li & Waters, 1998;Miyabe et al, 2000), have a lethal phenotype following cold or heat shock (Giangrossi et al, 2002;Wada et al, 1988), are defective in cell division (Dri et al, 1991) and are altered in outermembrane protein composition (Painbeni et al, 1997). Recently, the HU regulon was determined in E. coli using transcription profiling of strains deficient in the alpha, beta, or both HU subunits (Oberto et al, 2009). This study discovered that HU affects expression of 8 % of the E. coli genome.…”

“…Thus, PG0121 is expressed in all phases of growth, but is encoded in different transcripts. Furthermore, the data indicate that when HU is expressed from its own promoter, expression of the capsule operon is either off or at very low levels.Expression of genes involved in synthesis of surface polysaccharides, cell division, iron acquisition and DNA binding are altered in a PG0121 HU mutant during mid-exponential growth phaseIt was recently determined that HU protein is a master regulator in E. coli; controlling genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction (Oberto et al, 2009). Our previous studies determined that PG0121 (HUb) expression affects production of K-antigen capsule in P. gingivalis (Alberti-Segui et al, 2010).…”