- Volume 165, Issue 1, 2019

We studied Escherichia coli BW25113 growth in a complex medium with emphasis on amino acid consumption. The aim was to profile amino acid utilization in acid-hydrolysed casein and a defined nutrient-rich medium and based on these measurements modify the medium for better growth performance. Amino acid depletions in both media caused apparent biomass growth stops that prolonged growth duration. Obtained amino acid consumption values enabled a new defined medium to be formulated, where no growth stops were observed, the specific growth rate was constant, and the provided substrates were fully utilized. Similarly, we modified the acid-hydrolysed casein medium by adding pure amino acids that removed the apparent biomass growth stops. Key to our results was the combination of growth medium analysis and process monitoring data, specifically oxygen partial pressure and produced carbon dioxide that were used to track growth changes. Our findings showed the deficiencies of the nutrient-rich medium and how rational medium design, based on consumption values, removed these shortcomings. The resulting balanced medium gives a high specific growth rate and is suitable for studying E. coli physiology at fast growth.

Escherichia coli strain 15 (ATCC 9723) formed robust biofilms of two distinct forms on glass tubes. In rich, low-osmolarity medium, the biofilms were restricted to the air/liquid interface, resulting in rings attached to the glass. As it was not evident that these biofilms extended across the liquid surface, we termed them ‘ring’ rather than ‘pellicle’ biofilms. In minimal medium supplemented with a non-fermentable substrate as the carbon/energy source, we observed either robust ring biofilms or little biofilm of any type, depending on the substrate. In contrast, fermentable substrates (sugars and sugar derivatives) supported robust biofilms covering most of the solid/liquid interface, which we termed ‘tube-covering biofilms’. Maximal biofilm growth was observed when the sugar was a relatively poor substrate, supporting slow growth and known to cause minimal dephosphorylation of regulatory protein Enzyme IIAGlucose of the phosphotransferase system. Compounds found to be inhibitors of biofilm growth, such as lactate, caused a shift from tube-covering to ring form at low concentration and complete loss of biofilm growth at high when added to minimal medium supplemented with a fermentable substrate. Exogenous cAMP activated biofilm growth under all conditions tested, leading to more intense ring or tube-covering biofilms and/or to a shift from ring to tube-covering form.

The binding sites of YihW, an uncharacterized DeoR-family transcription factor (TF) of Escherichia coli K-12, were identified using Genomic SELEX screening at two closely located sites, one inside the spacer between the bidirectional transcription units comprising the yihUTS operon and the yihV gene, and another one upstream of the yihW gene itself. Recently the YihUTS and YihV proteins were identified as catalysing the catabolism of sulfoquinovose (SQ), a hydrolysis product of sulfoquinovosyl diacylglycerol (SQDG) derived from plants and other photosynthetic organisms. Gel shift assay in vitro and reporter assay in vivo indicated that YihW functions as a repressor for all three transcription units. De-repression of the yih operons was found to be under the control of SQ as inducer, but not of lactose, glucose or galactose. Furthermore, a mode of its cooperative DNA binding was suggested for YihW by atomic force microscopy. Hence, as a regulator of the catabolism of SQ, we renamed YihW as CsqR.

Two component systems, composed of a receptor histidine kinase and a cytoplasmic response regulator, regulate pivotal cellular processes in microorganisms. Here we describe a new screening procedure for the identification of amino acids that are crucial for the functioning of DesK, a prototypic thermosensor histidine kinase from Bacillus subtilis. This experimental strategy involves random mutagenesis of the membrane sensor domain of the DesK coding sequence, followed by the use of a detection procedure based on changes in the colony morphogenesis that take place during the sporulation programme of B. subtilis. This method permitted us the recovery of mutants defective in DesK temperature sensing. This screening approach could be applied to all histidine kinases of B. subtilis and also to kinases of other bacteria that are functionally expressed in this organism. Moreover, this reporter assay could be expanded to develop reporter assays for a variety of transcriptionally regulated systems.

Expression of cholera toxin (CT), the principal virulence factor of the cholera pathogen Vibrio cholerae, is positively modulated by the RNA polymerase binding unusual transcription factor DksA (DksA_Vc) of the stringent response pathway. Here we report that even though CT (encoded by the genes ctxAB) production is downregulated in the V. cholerae ΔdksA (ΔdksA_Vc ) mutant, the expression of the ctxA gene as well as the genes encoding different virulence regulators, namely, AphA, TcpP and ToxT, were also upregulated. Since DksA_Vc positively regulates HapR, a known negative regulator of CT production, the increased expression of different virulence genes in ΔdksA_Vc was due most probably to downregulation of HapR. There was no secretion/transport-related defect in ΔdksA_Vc cells because whole cell lysates of the mutant showed a negligible amount of CT accumulation similar to WT cells. To understand further, the hapR gene was deleted in ΔdksA_Vc background, however, the double mutant failed to rescue the CT production defect suggesting strongly towards post-transcriptional/translational regulation by DksA_Vc. This hypothesis was further confirmed when the site-directed mutagenesis of each or both of the conserved aspartic acid residues at positions 68 and 71 of DksA_Vc, which are essential for transcription initiation during the stringent response, had no effect in the regulation of CT expression. Interestingly, progressive deletion analysis indicated that the C4-type Zn finger motif present in the C-terminus of DksA_Vc is essential for optimal CT production. Since this motif plays important roles in DNA/RNA binding, the present study indicates a novel complex post-transcriptional regulation of CT expression by DksA_Vc.

The Streptococcus mutans Cid/Lrg system represents an ideal model for studying this organism’s ability to withstand various stressors encountered in the oral cavity. The lrg and cid operons display distinct and opposite patterns of expression in response to growth phase and glucose levels, suggesting that the activity and regulation of these proteins must be tightly coordinated in the cell and closely associated with metabolic pathways of the organism. Here, we demonstrate that expression of the cid and lrg operons is directly mediated by a global transcriptional regulator CcpA in response to glucose levels. Comparison of the cid and lrg promoter regions with the conserved CcpA binding motif revealed the presence of two potential cre sites (for CcpA binding) in the cid promoter (designated cid-cre1 and cid-cre2), which were arranged in a similar manner to those previously identified in the lrg promoter region (designated lrg-cre1 and lrg-cre2). We demonstrated that CcpA binds to both the cid and lrg promoters with a high affinity, but has an opposing glucose-dependent effect on the regulation of cid (positive) and lrg (negative) expression. DNase I footprinting analyses revealed potential binding sequences for CcpA in both cid and lrg promoter regions. Collectively, these data suggest that CcpA is a direct regulator of cid and lrg expression, and are suggestive of a potential mechanism by which Cid/Lrg-mediated virulence and cellular homeostasis is integrated with signals associated with both the environment and cellular metabolic status.