Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas species

González, Nicolas; Heeb, Stephan; Valverde, Claudio; Kay, Elisabeth; Reimmann, Cornelia; Junier, Thomas; Haas, Dieter

doi:10.1186/1471-2164-9-167

Cited by 75 publications

(94 citation statements)

References 54 publications

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“…Twenty-two SNPs are transversions, and 17 SNPs are transitions. Nine SNPs are located in intergenic regions, of which SNP 5036891 resides within one of the noncoding RNA loci described so far (3,23,35). Of the 30 SNPs in coding regions, 13 are synonymous substitutions, 16 cause an amino acid exchange, and one changes an arginine into a stop codon.…”

Section: Resultsmentioning

confidence: 99%

Genome Diversity ofPseudomonas aeruginosaPAO1 Laboratory Strains

et al. 2010

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Pseudomonas aeruginosa PAO1 is the most commonly used strain for research on this ubiquitous and metabolically versatile opportunistic pathogen. Strain PAO1, a derivative of the original Australian PAO isolate, has been distributed worldwide to laboratories and strain collections. Over decades discordant phenotypes of PAO1 sublines have emerged. Taking the existing PAO1-UW genome sequence (named after the University of Washington, which led the sequencing project) as a blueprint, the genome sequences of reference strains MPAO1 and PAO1-DSM (stored at the German Collection for Microorganisms and Cell Cultures [DSMZ]) were resolved by physical mapping and deep short read sequencing-by-synthesis. MPAO1 has been the source of near-saturation libraries of transposon insertion mutants, and PAO1-DSM is identical in its SpeI-DpnI restriction map with the original isolate. The major genomic differences of MPAO1 and PAO1-DSM in comparison to PAO1-UW are the lack of a large inversion, a duplication of a mobile 12-kb prophage region carrying a distinct integrase and protein phosphatases or kinases, deletions of 3 to 1,006 bp in size, and at least 39 single-nucleotide substitutions, 17 of which affect protein sequences. The PAO1 sublines differed in their ability to cope with nutrient limitation and their virulence in an acute murine airway infection model. Subline PAO1-DSM outnumbered the two other sublines in late stationary growth phase. In conclusion, P. aeruginosa PAO1 shows an ongoing microevolution of genotype and phenotype that jeopardizes the reproducibility of research. High-throughput genome resequencing will resolve more cases and could become a proper quality control for strain collections.The metabolically versatile Pseudomonas aeruginosa is an opportunistic pathogen of plants, animals, and humans and is ubiquitously distributed in soil and aquatic habitats. The common reference strain is P. aeruginosa PAO1, a spontaneous chloramphenicol-resistant mutant of the original PAO strain (earlier called "P. aeruginosa strain 1") that had been isolated in 1954 from a wound in Melbourne, Australia (9, 10). This PAO1 strain from Bruce Holloway's laboratory has become the reference strain for Pseudomonas genetics and functional analyses of the physiology and metabolism of this gammaproteobacterium. A genetic map of its chromosome was generated by exploiting the mechanisms of gene exchange in bacteria, i.e., transduction and conjugation (11). With the advent of pulsedfield gel electrophoresis (PFGE), a physical map of the PAO1 genome was constructed (32) and later merged with the genetic map information (12). By 2000 the PAO1 strain had been completely sequenced (36). Thereafter, the genome annotation has been continually updated and the database content and functionality have been expanded to facilitate accelerated discovery of P. aeruginosa drug targets and vaccine candidates (38). Two near-saturation libraries of transposon insertion mutants have been constructed in P. aeruginosa PAO1 as a global resource for the scient...

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Section: Resultsmentioning

confidence: 99%

Genome Diversity ofPseudomonas aeruginosaPAO1 Laboratory Strains

et al. 2010

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“…The most likely options are that CinS acts as a DNA-or RNA-binding protein that can enhance gene expression or RNA levels. There are several RNA-binding proteins that can influence quorum-sensing regulation in other bacteria (18,22,46,48), sometimes circumventing the quorum-sensing regulatory system (21). However, there is also evidence for small DNA-binding proteins playing a role in quorum-sensing regulation (30) and a small quorum-sensing-induced protein (DegQ) that stimulates phosphotransfer to a transcriptional regulator that affects motility and biofilm formation (26).…”

Section: Discussionmentioning

confidence: 99%

ThecinandraiQuorum-Sensing Regulatory Systems inRhizobium leguminosarumAre Coordinated by ExpR and CinS, a Small Regulatory Protein Coexpressed with CinI

et al. 2009

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To understand how the Rhizobium leguminosarum raiI-raiR quorum-sensing system is regulated, we identified mutants with decreased levels of RaiI-made N-acyl homoserine lactones (AHLs). A LuxR-type regulator, ExpR, is required for raiR expression, and RaiR is required to induce raiI. Since raiR (and raiI) expression is also reduced in cinI and cinR quorum-sensing mutants, we thought CinI-made AHLs may activate ExpR to induce raiR. However, added CinI-made AHLs did not induce raiR expression in a cinI mutant. The reduced raiR expression in cinI and cinR mutants was due to lack of expression of cinS immediately downstream of cinI. cinS encodes a 67-residue protein, translationally coupled to CinI, and cinS acts downstream of expR for raiR induction. Cloned cinS in R. leguminosarum caused an unusual collapse of colony structure, and this was delayed by mutation of expR. The phenotype looked like a loss of exopolysaccharide (EPS) integrity; mutations in cinI, cinR, cinS, and expR all reduced expression of plyB, encoding an EPS glycanase, and mutation of plyB abolished the effect of cloned cinS on colony morphology. We conclude that CinS and ExpR act to increase PlyB levels, thereby influencing the bacterial surface. CinS is conserved in other rhizobia, including Rhizobium etli; the previously observed effect of cinI and cinR mutations decreasing swarming in that strain is primarily due to a lack of CinS rather than a lack of CinI-made AHL. We conclude that CinS mediates quorum-sensing regulation because it is coregulated with an AHL synthase and demonstrate that its regulatory effects can occur in the absence of AHLs.

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“…In recent years, comparative genomics-based predictions have become a standard method to search for ncRNA genes conserved in at least two bacterial genomes (10,53,100,163,210,303,309). Thus, the high number of genome sequences from marine picocyanobacteria provides an excellent data set for the computational prediction of ncRNA genes.…”

Section: Two-component Systems and Crp-type Regulatorsmentioning

confidence: 99%

Ecological Genomics of Marine Picocyanobacteria

Scanlan

Ostrowski

Mazard

et al. 2009

Microbiol Mol Biol Rev

646

824

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SUMMARY Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45°N to 40°S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.

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Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas species

Cited by 75 publications

References 54 publications

Genome Diversity ofPseudomonas aeruginosaPAO1 Laboratory Strains

Genome Diversity ofPseudomonas aeruginosaPAO1 Laboratory Strains

ThecinandraiQuorum-Sensing Regulatory Systems inRhizobium leguminosarumAre Coordinated by ExpR and CinS, a Small Regulatory Protein Coexpressed with CinI

Ecological Genomics of Marine Picocyanobacteria

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