Comparing insertion libraries in two Pseudomonas aeruginosa strains to assess gene essentiality

Conceptual Model of Biofilm Antibiotic Tolerance That Integrates Phenomena of Diffusion, Metabolism, Gene Expression, and Physiology

Transcriptomic, metabolomic, physiological, and computational modeling approaches were integrated to gain insight into the mechanisms of antibiotic tolerance in an in vitro biofilm system. Pseudomonas aeruginosa biofilms were grown in drip flow reactors on a medium composed to mimic the exudate from a chronic wound. After 4 days, the biofilm was 114 μm thick with 9.45 log₁₀ CFU cm^-2 These biofilms exhibited tolerance, relative to exponential-phase planktonic cells, to subsequent treatment with ciprofloxacin. The specific growth rate of the biofilm was estimated via elemental balances to be approximately 0.37 h^-1 and with a reaction-diffusion model to be 0.32 h^-1, or one-third of the maximum specific growth rate for planktonic cells. Global analysis of gene expression indicated lower transcription of ribosomal genes and genes for other anabolic functions in biofilms than in exponential-phase planktonic cells and revealed the induction of multiple stress responses in biofilm cells, including those associated with growth arrest, zinc limitation, hypoxia, and acyl-homoserine lactone quorum sensing. Metabolic pathways for phenazine biosynthesis and denitrification were transcriptionally activated in biofilms. A customized reaction-diffusion model predicted that steep oxygen concentration gradients will form when these biofilms are thicker than about 40 μm. Mutant strains that were deficient in Psl polysaccharide synthesis, the stringent response, the stationary-phase response, and the membrane stress response exhibited increased ciprofloxacin susceptibility when cultured in biofilms. These results support a sequence of phenomena leading to biofilm antibiotic tolerance, involving oxygen limitation, electron acceptor starvation and growth arrest, induction of associated stress responses, and differentiation into protected cell states.IMPORTANCE Bacteria in biofilms are protected from killing by antibiotics, and this reduced susceptibility contributes to the persistence of infections such as those in the cystic fibrosis lung and chronic wounds. A generalized conceptual model of biofilm antimicrobial tolerance with the following mechanistic steps is proposed: (i) establishment of concentration gradients in metabolic substrates and products; (ii) active biological responses to these changes in the local chemical microenvironment; (iii) entry of biofilm cells into a spectrum of states involving alternative metabolisms, stress responses, slow growth, cessation of growth, or dormancy (all prior to antibiotic treatment); (iv) adaptive responses to antibiotic exposure; and (v) reduced susceptibility of microbial cells to antimicrobial challenges in some of the physiological states accessed through these changes.

The novel two-component regulatory system BfiSR regulates biofilm development by controlling the small RNA rsmZ through CafA

The formation of biofilms by the opportunistic pathogen Pseudomonas aeruginosa is a developmental process governed by a novel signal transduction system composed of three two-component regulatory systems (TCSs), BfiSR, BfmSR, and MifSR. Here, we show that BfiSR-dependent arrest of biofilm formation coincided with reduced expression of genes involved in virulence, posttranslational/transcriptional modification, and Rhl quorum sensing but increased expression of rhlAB and the small regulatory RNAs rsmYZ. Overexpression of rsmZ, but not rsmY, coincided with impaired biofilm development similar to inactivation of bfiS and retS. We furthermore show that BfiR binds to the 5' untranslated region of cafA encoding RNase G. Lack of cafA expression coincided with impaired biofilm development and increased rsmYZ levels during biofilm growth compared to the wild type. Overexpression of cafA restored ΔbfiS biofilm formation to wild-type levels and reduced rsmZ abundance. Moreover, inactivation of bfiS resulted in reduced virulence, as revealed by two plant models of infection. This work describes the regulation of a committed biofilm developmental step following attachment by the novel TCS BfiSR through the suppression of sRNA rsmZ via the direct regulation of RNase G in a biofilm-specific manner, thus underscoring the importance of posttranscriptional mechanisms in controlling biofilm development and virulence.

The Pho regulon influences biofilm formation and type three secretion in Pseudomonas aeruginosa

Research into the molecular mechanisms of the switch from highly motile to biofilm forming Pseudomonas fluorescens bacteria recently uncovered a role of inorganic phosphate as an important environmental regulatory factor to control c-di-GMP levels in the cell. In this study we present evidence that in the opportunistic pathogen P. aeruginosa the Pho regulon inhibits biofilm formation and is required for the repression of the type three secretion system. We furthermore identified an EAL domain protein as a downstream effector of the Pho regulon, which at least partially mediated the observed inhibition. Interestingly, inhibition of the P. aeruginosa virulence phenotype was Pho regulon-dependent in both a PA14 and a PAO1 strain background; however, in PA14 this inhibition was independent on the availability of inorganic phosphate, whereas in PAO1 phosphate enhanced biofilm formation independently of the inhibitory activity of the Pho regulon. These results clearly show that the Pho regulon contributes to the expression of the virulence phenotype in P. aeruginosa and add even more complexity to the strain-specific regulation of bacterial behaviour by environmental cues.

Chemical tools for dissecting bacterial physiology and virulence

Increasingly, chemical biology is being used in the context of bacterial virulence and the host-pathogen interaction, as small molecule inhibitors provide a number of unique advantages for the study of bacterial pathogens that complement powerful, existing classical genetic approaches. Small molecules have the potential to inhibit targets rapidly and reversibly, with a high degree of specificity. They are therefore well suited for studying the role of essential genes in bacterial physiology and virulence in both genetically tractable and intractable organisms, with the capacity to reveal novel phenotypes and insights into the function of essential factors during infection. The use of small molecule inhibitors during infection is also deepening our understanding of the role that host factors play in bacterial pathogenesis. In the future, the utility of chemical biology will grow as technologies for rapid identification of targets of interesting bioactive small molecules are developed. In this review, we highlight recent work in which small molecule inhibitors are used to study essential genes and genetically intractable organisms, to reveal novel phenotypes related to bacterial physiology, and to probe the role of bacterial and host factors during infection. In addition, we review recent advances in biochemical, genetic, and genomic techniques for target identification.

Using PATIMDB to create bacterial transposon insertion mutant libraries

PATIMDB is a software package for facilitating the generation of transposon mutant insertion libraries. The software has two main functions: process tracking and automated sequence analysis. The process tracking function specifically includes recording the status and fates of multiwell plates and samples in various stages of library construction. Automated sequence analysis refers specifically to the pipeline of sequence analysis starting with ABI files from a sequencing facility and ending with insertion location identifications. The protocols in this unit describe installation and use of PATIMDB software.