Differential Regulation of Genes for Cyclic-di-GMP Metabolism Orchestrates Adaptive Changes During Rhizosphere Colonization by Pseudomonas fluorescens

Abstract

Bacteria belonging to the Pseudomonas genus are highly successful colonizers of the plant rhizosphere. The ability of different Pseudomonas species to live either commensal lifestyles or to act as agents of plant-growth promotion or disease is reflected in a large, highly flexible accessory genome. Nevertheless, adaptation to the plant environment involves a commonality of phenotypic outputs such as changes to motility, coupled with synthesis of nutrient uptake systems, stress-response molecules and adherence factors including exopolysaccharides. Cyclic-di-GMP (cdG) is a highly important second messenger involved in the integration of environmental signals with appropriate adaptive responses and is known to play a central role in mediating effective rhizosphere colonization. In this study, we examined the transcription of multiple, reportedly plant-upregulated cdG metabolism genes during colonization of the wheat rhizosphere by the plant-growth-promoting strain P. fluorescens SBW25. While transcription of the tested genes generally increased in the rhizosphere environment, we additionally observed a tightly orchestrated response to environmental cues, with a distinct transcriptional pattern seen for each gene throughout the colonization process. Extensive phenotypical analysis of deletion and overexpression strains was then conducted and used to propose cellular functions for individual cdG signaling genes. Finally, in-depth genetic analysis of an important rhizosphere colonization regulator revealed a link between cdG control of growth, motility and stress response, and the carbon sources available in the rhizosphere.

Control of mRNA translation by dynamic ribosome modification

“…Bacterial adaptation to complex natural environments is controlled by an intricate series of connected signalling pathways that function both within individual cells and on the microbial community as a whole [11,14,26]. In addition to extensive transcriptional [6,11] and protein functional regulation [12], control of mRNA translation is critical for effective colonisation of plant rhizospheres [7]. In this study we characterise the RimABK pathway in Pseudomonas fluorescens and present evidence for the role that this novel translational regulatory system plays during bacterial adaptation to the rhizosphere environment through specific, controlled modification of a ribosomal protein.…”

“…This requires an interconnected network of signal transduction systems functioning at multiple regulatory levels, including gene transcription [6], modulation of translational activity [7] and changes in protein function [8]. The cyclic-di-GMP (cdG) signalling network mediates the switch between motile and sessile lifestyles in many bacterial species [9] and is a key regulator of rhizosphere colonisation in multiple plant-associated microbes [10][11][12][13]. CdG signalling in Pseudomonas forms a highly complex, non-linear and pleiotropic network, with multiple connections to other signalling systems and phenotypic outputs that vary profoundly in response to environmental cues [14,15].…”

“…CdG signalling in Pseudomonas forms a highly complex, non-linear and pleiotropic network, with multiple connections to other signalling systems and phenotypic outputs that vary profoundly in response to environmental cues [14,15]. The model P. fluorescens strain SBW25, for example, contains over 40 cdG-metabolic enzymes [16] that influence phenotypes at every regulatory level and whose expression varies throughout rhizosphere colonisation [11]. Pseudomonas cdG signalling shows extensive overlap with other global gene regulators, such as Gac/Rsm [17,18] and the RNA-chaperone Hfq [19].…”

Second messenger control of mRNA translation by dynamic ribosome modification

“…Bacterial adaptation to complex natural environments is controlled by an intricate series of connected signalling pathways that function both within individual cells and on the microbial community as a whole (22, 25, 44). In addition to extensive transcriptional (17, 22) and protein functional regulation (23), control of mRNA translation is critical for effective colonisation of plant rhizospheres (18). In this study we characterise the RimABK pathway in Pseudomonas fluorescens ; a novel translational regulatory system that controls bacterial adaptation to the rhizosphere environment through specific, controlled modification of a ribosomal protein.…”

“…CdG signalling in Pseudomonas forms a highly complex, non-linear and pleiotropic network, with multiple connections to other signalling systems and phenotypic outputs that vary profoundly in response to environmental cues (25, 26). The model P. fluorescens strain SBW25, for example, contains over 40 cdG-metabolic enzymes (27) that influence phenotypes at every regulatory level and whose expression varies throughout rhizosphere colonisation (22). Pseudomonas cdG signalling shows extensive overlap with other global gene regulators, such as Gac/Rsm (28, 29) and the RNA-chaperone Hfq (30).…”