Academic literature on the topic 'RRNPP systems'

Gram-positive bacteria carry out intercellular communication using secreted peptides. Important examples of this type of communication are the enterococcal sex pheromone systems, in which the transfer of conjugative plasmids is controlled by intercellular signaling among populations of donors and recipients. This review focuses on the pheromone response system of the conjugative plasmid pCF10. The peptide pheromones regulating pCF10 transfer act by modulating the ability of the PrgX transcription factor to repress the transcription of an operon encoding conjugation functions. Many Gram-positive bacteria regulate important processes, including the production of virulence factors, biofilm formation, sporulation, and genetic exchange using peptide-mediated signaling systems. The key master regulators of these systems comprise the RRNPP (RggRap/NprR/PlcR/PrgX) family of intracellular peptide receptors; these regulators show conserved structures. While many RRNPP systems include a core module of two linked genes encoding the regulatory protein and its cognate signaling peptide, the enterococcal sex pheromone plasmids have evolved to a complex system that also recognizes a second host-encoded signaling peptide. Additional regulatory genes not found in most RRNPP systems also modulate signal production and signal import in the enterococcal pheromone plasmids. This review summarizes several structural studies that cumulatively demonstrate that the ability of three pCF10 regulatory proteins to recognize the same 7-amino-acid pheromone peptide arose by convergent evolution of unrelated proteins from different families. We also focus on the selective pressures and structure/function constraints that have driven the evolution of pCF10 from a simple, single-peptide system resembling current RRNPPs in other bacteria to the current complex inducible plasmid transfer system.

The strictly anaerobic bacterium Clostridium acetobutylicum is well known for its ability to convert sugars into organic acids and solvents, most notably the potential biofuel butanol. However, the regulation of its fermentation metabolism, in particular the shift from acid to solvent production, remains poorly understood. The aim of this study was to investigate whether cell–cell communication plays a role in controlling the timing of this shift or the extent of solvent formation. Analysis of the available C. acetobutylicum genome sequences revealed the presence of eight putative RRNPP-type quorum-sensing systems, here designated qssA to qssH, each consisting of an RRNPP-type regulator gene followed by a small open reading frame encoding a putative signalling peptide precursor. The identified regulator and signal peptide precursor genes were designated qsrA to qsrH and qspA to qspH, respectively. Triplicate regulator mutants were generated in strain ATCC 824 for each of the eight systems and screened for phenotypic changes. The qsrB mutants showed increased solvent formation during early solventogenesis and hence the QssB system was selected for further characterization. Overexpression of qsrB severely reduced solvent and endospore formation and this effect could be overcome by adding short synthetic peptides to the culture medium representing a specific region of the QspB signalling peptide precursor. In addition, overexpression of qspB increased the production of acetone and butanol and the initial (48 h) titre of heat-resistant endospores. Together, these findings establish a role for QssB quorum sensing in the regulation of early solventogenesis and sporulation in C. acetobutylicum .

Paenibacillus polymyxa is an agriculturally important plant growth–promoting rhizobacterium. Many Paenibacillus species are known to be engaged in complex bacteria–bacteria and bacteria–host interactions, which in other species were shown to necessitate quorum sensing communication. However, to date, no quorum sensing systems have been described in Paenibacillus. Here, we show that the type strain P. polymyxa ATCC 842 encodes at least 16 peptide-based communication systems. Each of these systems is comprised of a pro-peptide that is secreted to the growth medium and processed to generate a mature short peptide. Each peptide has a cognate intracellular receptor of the RRNPP family, and we show that external addition of P. polymyxa communication peptides leads to reprogramming of the transcriptional response. We found that these quorum sensing systems are conserved across hundreds of species belonging to the Paenibacillaceae family, with some species encoding more than 25 different peptide-receptor pairs, representing a record number of quorum sensing systems encoded in a single genome.

In streptococci, intracellular quorum sensing pathways are based on quorum-sensing systems that are responsible for peptide secretion, maturation, and reimport. These peptides then interact with Rgg or ComR transcriptional regulators in the Rap, Rgg, NprR, PlcR, and PrgX (RRNPP) family, whose members are found in Gram-positive bacteria. Short hydrophobic peptides (SHP) interact with Rgg whereas ComS peptides interact with ComR regulators. To date, in Streptococcus thermophilus, peptide secretion, maturation, and extracellular fate have received little attention, even though this species has several (at least five) genes encoding Rgg regulators and one encoding a ComR regulator. We studied pheromone export in this species, focusing our attention on PptAB, which is an exporter of signaling peptides previously identified in Enterococcus faecalis, pathogenic streptococci and Staphylococcus aureus. In the S. thermophilus strain LMD-9, we showed that PptAB controlled three regulation systems, two SHP/Rgg systems (SHP/Rgg1358 and SHP/Rgg1299), and the ComS/ComR system, while using transcriptional fusions and that PptAB helped to produce and export at least three different mature SHPs (SHP1358, SHP1299, and SHP279) peptides while using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Using a deep sequencing approach (RNAseq), we showed that the exporter PptAB, the membrane protease Eep, and the oligopeptide importer Ami controlled the transcription of the genes that were located downstream from the five non-truncated rgg genes as well as few distal genes. This led us to propose that the five non-truncated shp/rgg loci were functional. Only three shp genes were expressed in our experimental condition. Thus, this transcriptome analysis also highlighted the complex interconnected network that exists between SHP/Rgg systems, where a few homologous signaling peptides likely interact with different regulators.

ABSTRACT rRNA transcription in Escherichia coli is activated by the FIS protein, which binds upstream of rrnp 1promoters and interacts directly with RNA polymerase. Analysis of the contribution of FIS to rrn transcription under changing physiological conditions is complicated by several factors: the wide variation in cellular FIS concentrations with growth conditions, the contributions of several other regulatory systems to rRNA synthesis, and the pleiotropy of fis mutations. In this report, we show by in vivo footprinting and Western blot analysis that occupancy of the rrnBp 1 FIS sites correlates with cellular levels of FIS. We find, using two methods of measurement (pulse induction of a FIS-activated hybrid promoter and primer extension from an unstable transcript made fromrrnBp 1), that the extent of transcription activation by FIS parallels the degree of FIS site occupancy and therefore cellular FIS levels. FIS activates transcription throughout exponential growth at low culture density, butrrnp 1 transcription increases independently of FIS immediately following upshift, before FIS accumulates. These results support the model that FIS is one of a set of overlapping signals that together contribute to transcription fromrrnp 1 promoters during steady-state growth.

Abstract An automated, rapidly relocatable nowcasting and prediction system, whose cornerstone is the full-physics, nested-grid, nonhydrostatic fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5), has been under development at the Pennsylvania State University since the late 1990s. In the applications presented in this paper, the Rapidly Relocatable Nowcast-Prediction System (RRNPS) provides a continuous stream of highly detailed nowcasts, defined here as gridded meteorological fields produced by a high-resolution mesoscale model assimilating available observations and staying just ahead of the clock to provide immediately available current meteorological conditions. The RRNPS, configured to use 36-, 12-, and 4-km nested domains, is applied over the Great Plains for 18 case days in August 2001, over the East Coast region for 8 case days in April 2002, and for 12 case days during the winter and summer of 2003. The performance of the RRNPS is evaluated using subjective and statistical methods for runs with and without the use of continuous four-dimensional data assimilation (FDDA). A statistical evaluation of the dependence of RRNPS skill on the length of model integration yields further insight into the value added by FDDA in RRNPS nowcasts. It must be emphasized that unlike typical operational analysis systems, none of the current data are used in the nowcasts since the nowcasts are made available just ahead of the clock for immediate use. Because none of the verification data are assimilated into the RRNPS at the time of verification, this evaluation is a true test of the time-integrated effects of previous FDDA on current model solutions. Furthermore, the statistical evaluations also utilize independent data completely withheld from the system at all times. Evaluation of the RRNPS versus observations on the 4- and 12-km grids shows that there is little difference in statistical skill between the two resolutions for the two application regions. However, subjective case evaluations indicate that mesoscale detail is added to the wind and mass fields on the 4-km domain of the RRNPS as compared to the coarser 12-km domain. Statistics suggest that 4-km resolution provides slightly more accurate meteorology for the domain including complex terrain and coastlines. The statistics also show that the use of continuous FDDA in a high-resolution mesoscale model improves the accuracy of the RRNPS nowcasts, and that this unique nowcast prediction system provides immediately available forecast-analysis products that are comparable or superior to those produced at operational centers, especially for the surface and the boundary layer. Finally, the RRNPS is also designed to run locally and on demand in a highly automated mode on modest computing platforms (e.g., a dual-processor PC) with potentially very limited data resources and nonstandard data communications.

El propósito de este trabajo es identificar los procesos de Relaciones Públicas involucrados en los sistemas de inteligencia estratégica de las organizaciones. Para ello se ha realizado estudio exploratorio, basado en revisión documental y mapeo comparativo de co-palabras entre la TS 16555-2 y los modelos de relaciones públicas. Con ello se pretende mostrar la pertinencia de las RRPP en los procesos de inteligencia estratégica vía especificaciones técnicas recogidas en procesos de sistematización y normalización para reforzar el papel que las RRPP desempeñan en el marco de retos y oportunidades para la estrategia empresarial en el contexto actual. Public relations and strategic intelligence. A study of similar processes in models of public relations and the TS16555-2 technical specification approved by the European Committee for Standardization Technical Committee CEN/TC 389 Abstract In this article we aim to identify public relations processes in organisation strategic intelligence systems. An exploratory analysis is carried out, based on review of documents and comparative mapping of words in TS16555-2 and models of public relations. The aim is to establish the pertinence of public relations in strategic intelligence processes through technical specifications in standardization and normalization processes, in order to show how public relations processes have become increasingly important in response to the demands and opportunities of strategic intelligence work in organisations today. Keywords Public relations, strategic intelligence, standardization, innovation management.

Abstract Gram-positive Firmicutes bacteria and their mobile genetic elements (plasmids, bacteriophages) encode peptide-based quorum sensing systems (QSSs) that orchestrate behavioral transitions as a function of population densities. In their simplest form, termed “RRNPP”, these QSSs are composed of two adjacent genes: a communication propeptide and its cognate intracellular receptor. RRNPP QSSs notably regulate social/competitive behaviors such as virulence or biofilm formation in bacteria, conjugation in plasmids or lysogeny in temperate bacteriophages. However, the genetic diversity and the prevalence of these communication systems, together with the breadth of behaviors they control, remain largely under-appreciated. To better assess the impact of density-dependency on microbial community dynamics and evolution, we developed the RRNPP_detector software, which predicts known and novel RRNPP QSSs in chromosomes, plasmids and bacteriophages of Firmicutes. Applying RRNPP_detector against available complete genomes of viruses and Firmicutes, we identified a rich repertoire of RRNPP QSSs from 11 already-known subfamilies and 21 novel high-confidence candidate subfamilies distributed across a vast diversity of taxa. The analysis of high-confidence RRNPP subfamilies notably revealed 14 subfamilies shared between chromosomes/plasmids/phages, 181 plasmids and 82 phages encoding multiple communication systems, phage-encoded QSSs predicted to dynamically modulate bacterial behaviors, and 196 candidate biosynthetic gene clusters under density-dependent regulation. Overall, our work enhances the field of quorum sensing research and reveals novel insights into the co-evolution of gram-positive bacteria and their mobile genetic elements.

Oligopeptide-permeases (Opps) are used by bacteria to import short peptides. In addition to their metabolic benefit, imported short peptides are used in many Gram-positive bacteria as signalling molecules of the RRNPP super-family of quorum-sensing systems, making Opps an integral part of cell–cell communication. In some Gram-positive bacteria there exist multiple Opps and the relative importance of those to RRNPP quorum sensing are not fully clear. Specifically, in Bacillus subtilis , the Gram-positive model species, there exist two homologous oligopeptide permeases named Opp and App. Previous work showed that the App system is mutated in lab strain 168 and its recovery partially complements an Opp mutation for several developmental processes. Yet, the nature of the impact of App on signalling and development in wild-type strains, where both permeases are active was not studied. Here we re-examine the impact of the two permease systems. We find that App has a minor contribution to biofilm formation, surfactin production and phage infection compared to the effect of Opp. This reduced effect is also reflected in its lower ability to import the signals of four different Rap-Phr RRNPP systems. Further analysis of the App system revealed that, unlike Opp, some App genes have undergone horizontal transfer, resulting in two distinct divergent alleles of this system in B. subtilis strains. We found that both alleles were substantially better adapted than the Opp system to import an exogenous RRNPP signal of the Bacillus cereus group PlcR-PapR system. In summary, we find that the App system has only a minor role in signalling but may still be crucial for the import of other peptides.

ABSTRACT In bacterial populations, quorum sensing (QS) systems participate in the regulation of specialization processes and regulate collective behaviors that mediate interactions and allow survival of the species. In Gram-positive bacteria, QS systems of the RRNPP family (Rgg, Rap, NprR, PlcR, and PrgX) consist of intracellular receptors and their cognate signaling peptides. Two of these receptors, Rap and NprR, have regained attention in Bacillus subtilis and the Bacillus cereus group. Some Rap proteins, such as RapH and Rap60, are multifunctional and/or redundant in function, linking the specialization processes of sporulation and competence, as well as global expression changes in the transition phase in B. subtilis. NprR, an evolutionary intermediate between Rap and RRNPP transcriptional activators, is a bifunctional regulator that modulates sporulation initiation and activates nutrient scavenging genes. In this review, we discuss how these receptors switch between functions and connect distinct signaling pathways. Based on structural evidence, we propose that RapH and Rap60 should be considered moonlighting proteins. Additionally, we analyze an evolutionary and ecological perspective to understand the multifunctionality and functional redundancy of these regulators in both Bacillus spp. and non-Bacillus Firmicutes. Understanding the mechanistic, structural, ecological, and evolutionary basis for the multifunctionality and redundancy of these QS systems is a key step for achieving the development of innovative technologies for health and agriculture.

Les systèmes de « Quorum Sensing » (QSSs) sont des systèmes génétiques permettant la communication entre cellules ou entre bactériophages. Cette communication est réalisée par l’émission et la détection d’une molécule signal dont la concentration extracellulaire reflète la densité de la population codant le QSS. Les QSSs ont une importance capitale dans la régulation densité-dépendante de processus biologiques clés tels que la virulence, la sporulation ou la formation de biofilms chez les bactéries, la conjugaison chez les plasmides, ou la lysogénie chez les bactériophages tempérés. Néanmoins, la diversité des QSSs demeure largement sous-explorée et il en va de même pour celle des organismes, plasmides et virus codant ces systèmes. Ainsi, beaucoup de comportements microbiens/viraux régulés de façon densité-dépendante restent probablement à découvrir, dont certains pourraient peut-être révolutionner notre vision de l’adaptation microbienne et de la coévolution entre bactéries et leurs éléments génétiques mobiles. Précisément, cette thèse de bioinformatique évolutive explore les diversités phylogénétique et fonctionnelle du processus de détection du quorum par des méthodes d’analyses de génomes et de réseaux appliquées à des éléments génétiques traditionnellement délaissés par ce champ de recherche : génomes de lignées méconnues comme les CPRs et les DPANNs, métagénomes environnementaux, génomes viraux ou encore plasmides. En particulier, cette thèse pose les bases théoriques de l’inférence de réseaux de communication au sein de communautés microbiennes environnementales et inclut le développement d’une nouvelle méthode permettant l’identification de QSSs de type RRNPP (Rap-Rgg-NprR-PlcR-PrgX) non homologues à des QSSs déjà connus. Ce travail révèle notamment les premiers bactériophages bilingues, c’est-à-dire codant deux QSSs appartenant à des familles génétiques différentes ainsi que les premiers bactériophages prédits pour manipuler de façon densité-dépendante la biologie de leur hôte bactérien
Quorum sensing systems (QSSs) are genetic systems supporting cell-cell or bacteriophage-bacteriophage communication via the production and the detection of a signal molecule, the extracellular concentration of which reflects the density of the QSS-encoding population. QSSs have a prime importance in the regulation of key biological processes such as virulence, sporulation or biofilm formation in bacteria, conjugation in plasmids or lysogeny in temperate bacteriophages. However, the genetic diversity of QSSs remains largely underexplored and the same holds for the diversity of organisms, plasmids and viruses encoding these systems. Hence, many bacterial and viral density-dependent behaviors likely await to be discovered, some of which could perhaps transform our views of microbial adaptation and of the co-evolution between bacteria and their mobile genetic elements. Specifically, this PhD in evolutionary bioinformatics explores the phylogenetic and functional diversity of quorum sensing using genome and network analysis methods applied to genetic elements traditionally neglected by this research field: genomes of poorly known lineages such as CPRs and DPANNs, environmental metagenomes, viral genomes or plasmids. In particular, this thesis lays the theoretical foundations for the inference of communication networks within environmental microbial communities and includes the development of a new method allowing the identification of QSSs of the RRNPP type (Rap-Rgg-NprR-PlcR-PrgX) that are non-homologous to already known QSSs. This work notably reveals the first bilingual bacteriophages, i.e. encoding two QSSs belonging to different genetic families, as well as the first bacteriophages predicted to manipulate in a density-dependent manner the biology of their bacterial host