Summary The ability of Pseudomonas species to thrive in all major natural environments (i.e. terrestrial, freshwater and marine) is based on its exceptional capability to adapt to physicochemical changes. Thus, environmental bacteria have to tightly control the maintenance of numerous physiological traits across different conditions. The intracellular pH (pHi) homoeostasis is a particularly important feature, since the pHi influences a large portion of the biochemical processes in the cell. Despite its importance, relatively few reliable, easy‐to‐implement tools have been designed for quantifying in vivo pHi changes in Gram‐negative bacteria with minimal manipulations. Here we describe a convenient, non‐invasive protocol for the quantification of the pHi in bacteria, which is based on the ratiometric fluorescent indicator protein PHP (pH indicator for Pseudomonas). The DNA sequence encoding PHP was thoroughly adapted to guarantee optimal transcription and translation of the indicator in Pseudomonas species. Our PHP‐based quantification method demonstrated that pHi is tightly regulated over a narrow range of pH values not only in Pseudomonas, but also in other Gram‐negative bacterial species such as Escherichia coli. The maintenance of the cytoplasmic pH homoeostasis in vivo could also be observed upon internal (e.g. redirection of glucose consumption pathways in P. putida) and external (e.g. antibiotic exposure in P. aeruginosa) perturbations, and the PHP indicator was also used to follow dynamic changes in the pHi upon external pH shifts. In summary, our work describes a reliable method for measuring pHi in Pseudomonas, allowing for the detailed investigation of bacterial pHi homoeostasis and its regulation.

High levels of the universal bacterial second messenger cyclic di-GMP (c-di-GMP) promote the establishment of surface-attached growth in many bacteria. Not only can c-di-GMP bind to nucleic acids and directly control gene expression, but it also binds to a diverse array of proteins of specialized functions and orchestrates their activity. Since its development in the early 1990s, the synthetic peptide array technique has become a powerful tool for high-throughput approaches and was successfully applied to investigate the binding specificity of protein-ligand interactions. In this study, we used peptide arrays to uncover the c-di-GMP binding site of a Pseudomonas aeruginosa protein (PA3740) that was isolated in a chemical proteomics approach. PA3740 was shown to bind c-di-GMP with a high affinity, and peptide arrays uncovered LKKALKKQTNLR to be a putative c-di-GMP binding motif. Most interestingly, different from the previously identified c-di-GMP binding motif of the PilZ domain (RXXXR) or the I site of diguanylate cyclases (RXXD), two leucine residues and a glutamine residue and not the charged amino acids provided the key residues of the binding sequence. Those three amino acids are highly conserved across PA3740 homologs, and their singular exchange to alanine reduced c-di-GMP binding within the full-length protein.

The c-di-GMP-binding effector protein FlgZ has been demonstrated to control motility in the opportunistic pathogen Pseudomonas aeruginosa and it was suggested that c-di-GMP-bound FlgZ impedes motility via its interaction with the MotCD stator. To further understand how motility is downregulated in P. aeruginosa and to elucidate the general control mechanisms operating during bacterial growth, we examined the spatiotemporal activity of FlgZ. We re-annotated the P. aeruginosa flgZ open reading frame and demonstrated that FlgZ-mediated downregulation of motility is fine-tuned via three independent mechanisms. First, we found that flgZ gene is transcribed independently from flgMN in stationary growth phase to increase FlgZ protein levels in the cell. Second, FlgZ localizes to the cell pole upon c-di-GMP binding and third, we describe that FimV, a cell pole anchor protein, is involved in increasing the polar localized c-di-GMP bound FlgZ to inhibit both, swimming and swarming motility. Our results shed light on the complex dynamics and spatiotemporal control of c-di-GMP-dependent bacterial motility phenotypes and on how the polar anchor protein FimV, the motor brake FlgZ and the stator proteins function to repress flagella-driven swimming and swarming motility. Fig. 1. Growth phase-dependent transcription and translation of flgZ.A. FlgZ protein levels of P. aeruginosa PAO1 grown in exponential and stationary growth phase (adjusted to the same optical density) were determined by Western blot analysis using an anti-FlgZ antibody. B. Relative fold change of flgM, flgN and flgZ gene expression in stationary growth phase compared to exponential growth phase. Data were extracted from a previous publication (Dötsch et al., 2012). RNA sequencing was performed with cultures grown to OD 1 (exponential) and for 12 h (stationary). Both were sequenced in duplicates. The obtained sequences were mapped to the PA14 genome. Absolute read counts were normalized to yield nRPK (normalized reads per kilobase of gene sequence) values. C. A set of six primers was used in different combinations to PCR-amplify intragenic (1, 2, 3) and intergenic (4, 5) regions of the flgMNZ genes as indicated. D. Reverse Transcriptase PCR: cDNA was generated from RNA isolated from exponential (left) and from early stationary (right) growth phase. Lane 1-3 correspond to the intragenic PCR products of flgM (1), flgN (2), flgZ (3), lane 4-5 to the intergenic flgMN (4) and flgNZ (5) PCR products. As negative control (NC) total RNA was not subjected to reverse transcription.

C‐di‐GMP signaling can directly influence bacterial behavior by affecting the functionality of c‐di‐GMP‐binding proteins. In addition, c‐di‐GMP can exert a global effect on gene transcription or translation, for example, via riboswitches or by binding to transcription factors. In this study, we investigated the effects of changes in intracellular c‐di‐GMP levels on gene expression and protein production in the opportunistic pathogen Pseudomonas aeruginosa. We induced c‐di‐GMP production via an ectopically introduced diguanylate cyclase and recorded the transcriptional, translational as well as proteomic profile of the cells. We demonstrate that rising levels of c‐di‐GMP under growth conditions otherwise characterized by low c‐di‐GMP levels caused a switch to a non‐motile, auto‐aggregative P. aeruginosa phenotype. This phenotypic switch became apparent before any c‐di‐GMP‐dependent role on transcription, translation, or protein abundance was observed. Our results suggest that rising global c‐di‐GMP pools first affects the motility phenotype of P. aeruginosa by altering protein functionality and only then global gene transcription.