Identification and characterization of novel N-acylhomoserine lactonase from nonpathogenic Allorhizobium vitis, a candidate for biocontrol agent

Some strains of nonpathogenic Allorhizobium vitis can control crown gall disease in grapevines caused by pathogenic A. vitis and are considered candidates for biocontrol agents. Many plant pathogenic bacteria regulate the expression of their virulence genes via quorum sensing using N-acylhomoserine lactone (AHL) as a signaling compound. The eight nonpathogenic A. vitis strains used in this study showed AHL-degrading activity. The complete genome sequence of A. vitis MAFF 212306 contained three AHL lactonase gene homologs. When these genes were cloned and transformed into Escherichia coli DH5α, E. coli harboring the aiiV gene (RvVAR031_27660) showed AHL-degrading activity. The aiiV coding region was successfully amplified by polymerase chain reaction from the genomes of all eight strains of nonpathogenic A. vitis. Purified His-tagged AiiV exhibited AHL lactonase activity by hydrolyzing the lactone ring of AHL. AiiV had an optimal temperature of approximately 30 °C; however, its thermostability decreased above 40 °C. When the AiiV-expressing plasmid was transformed into Pectobacterium carotovorum subsp. carotovorum NBRC 3830, AHL production by NBRC 3830 decreased below the detection limit, and its maceration activity, which was controlled by quorum sensing, almost disappeared. These results suggest the potential use of AHL-degrading nonpathogenic A. vitis for the inhibition of crown gall disease in grapevines and other plant diseases controlled by quorum sensing.

Pectobacterium araliae sp. nov., a pathogen causing bacterial soft rot of Japanese angelica tree in Japan

Phytopathogenic bacteria (MAFF 302110T and MAFF 302107) were isolated from lesions on Japanese angelica trees affected by bacterial soft rot in Yamanashi Prefecture, Japan. The strains were Gram-reaction-negative, facultatively anaerobic, motile with peritrichous flagella, rod-shaped, and non-spore-forming. The genomic DNA G+C content was 51.1 mol % and the predominant cellular fatty acids included summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 2 (comprising any combination of C12 : 0 aldehyde, an unknown fatty acid with an equivalent chain length of 10.928, C16 : 1 iso I, and C14 : 0 3OH), and C12 : 0. Phylogenetic analyses based on 16S rRNA and gyrB gene sequences, along with phylogenomic analysis utilizing whole-genome sequences, consistently placed these strains within the genus Pectobacterium. However, their phylogenetic positions did not align with any known species within the genus. Comparative studies involving average nucleotide identity and digital DNA-DNA hybridization with the closely related species indicated values below the thresholds employed for the prokaryotic species delineation (95-96 % and 70 %, respectively), with the highest values observed for Pectobacterium polonicum DPMP315T (92.10 and 47.1 %, respectively). Phenotypic characteristics, cellular fatty acid composition, and a repertoire of secretion systems could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic, and genotypic data obtained in this study show that MAFF 302110T/MAFF 302107 represent a novel species of the genus Pectobacterium, for which we propose the name Pectobacterium araliae sp. nov., designating MAFF 302110T (=ICMP 25161T) as the type strain.

Pseudomonas solani sp. nov. isolated from the rhizosphere of eggplant in Japan

The search for bacteria that can be used as biocontrol agents to control crop diseases yielded a promising candidate, Sm006^T, which was isolated from the rhizosphere of eggplant (Solanum melongena) growing in a field in Aichi Prefecture, Japan, in 2006. The cells were Gram-stain-negative, aerobic, non-spore-forming, rod-shaped and motile with one polar flagellum. The results of homology searches and phylogenetic analyses based on the 16S rRNA gene sequence indicated that Sm006^T represents a member of the genus Pseudomonas. The genomic DNA G+C content was 66.3 mol% and the major cellular fatty acids (more than 5 % of the total fatty acids) were summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c), summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c), C_16 : 0 and C_12 : 0. Phylogenetic analyses using the rpoD gene sequence and phylogenomic analysis of the whole genome sequence revealed that Sm006^T represents a member of the Pseudomonas resinovorans group; however, its phylogenetic position does not match that of any known species of the genus Pseudomonas. The average nucleotide identity and digital DNA-DNA hybridisation values between the strain and closely related species were lower than the thresholds for prokaryotic species delineation (95-96 and 70 %, respectively), with the highest values observed for Pseudomonas tohonis TUM18999^T (92.05 and 46.3 %, respectively). Phenotypic characteristics, cellular fatty acid composition and possession of 2,4-diacetylphloroglucinol biosynthetic gene cluster could be used to differentiate the strain from its closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained during this study indicated that Sm006^T represents a novel species of the genus Pseudomonas, for which we propose the name Pseudomonas solani sp. nov., with Sm006^T (= MAFF 212523^T = ICMP 24689^T) as the type strain.

N -acylhomoserine lactone-degrading activity of Trichoderma species and its application in the inhibition of bacterial quorum sensing

Many gram-negative pathogens can activate virulence factors under the control of N-acylhomoserine lactone (AHL）-mediated quorum sensing. AHL-degrading enzymes have been investigated for their application in disease control. Trichoderma is a genus of fungi inhabiting various types of soil and are widely used as biocontrol agents for plant pathogens. When the AHL-degrading activity of 33 strains belonging to Trichoderma species was investigated, most strains can degrade AHL. AHL lactonase catalyzes AHL ring opening by hydrolyzing lactone. Two model strains, Trichoderma atroviride MAFF 242473 and MAFF 242475, degrade AHL using their AHL lactonase activity and rapidly metabolize ring-opening AHL. Moreover, co-inoculation with MAFF 242473 and MAFF 242475 effectively inhibited AHL production by the plant pathogens, Pantoea ananatis and Pectobacterium carotovorum subsp. carotovorum. Our study suggested that Trichoderma might be an effective biocontrol agent to inhibit the expression of virulence factors via AHL-mediated quorum sensing.

Genomic Reclassification and Phenotypic Characterization of Pseudomonas putida Strains Deposited in Japanese Culture Collections

Pseudomonas putida is a major species belonging to the genus Pseudomonas. Although several hundred strains of P. putida have been deposited in culture collections, they potentially differ from the genetically defined "true Pseudomonas putida" because many were classified as P. putida based on their phenotypic and metabolic characteristics. A phylogenetic ana-lysis based on the concatenated sequences of the 16S rRNA and rpoD genes revealed that 46 strains of P. putida deposited in Japanese culture collections were classified into nine operational taxonomic units (OTUs) and eleven singletons. The OTU7 strain produces N-acylhomoserine lactone as a quorum-sensing signal. One of the OTU7 strains, JCM 20066, exhibited a ppuI-rsaL-ppuR quorum-sensing system that controls biofilm formation and motility. The P. putida type strain JCM 13063^T and six other strains were classified as OTU4. Classification based on the calculation of whole-genome similarity revealed that three OTU4 strains, JCM 20005, 21368, and 13061, were regarded as the same species as JCM 13063^T and defined as true P. putida. When orthologous genes in the whole-genome sequences of true P. putida strains were screened, PP4_28660 from P. putida NBRC 14164^T (=JCM 13063^T) was present in all true P. putida genome sequences. The internal region of PP4_28660 was successfully amplified from all true P. putida strains using the specific primers designed in this study.

Regulation of phenazine-1-carboxamide production by quorum sensing in type strains of Pseudomonas chlororaphis subsp. chlororaphis and Pseudomonas chlororaphis subsp. piscium

Quorum sensing is a population density-dependent gene regulation mechanism. N-Acyl-l-homoserine lactone (AHL) has been identified as a signal compound in quorum sensing in gram-negative bacteria. Phenazine derivatives are bacterial secondary metabolites known for their broad-spectrum antifungal activity. Pseudomonas chlororaphis has been demonstrated to be a biocontrol strain, and most of its species can produce phenazine derivatives under AHL-mediated quorum sensing. Although P. chlororaphis is divided into four subspecies, the relationship between phenazine production and quorum sensing has not been investigated in two of the subspecies, P. chlororaphis subsp. chlororaphis and piscium. Two luxI/luxR homolog gene sets, phzI and phzR and csaI and csaR, were found in the complete genome sequences of the type strains of P. chlororaphis subsp. chlororaphis JCM 2778^T and P. chlororaphis subsp. piscium DSM 21509^T. Two major AHLs, N-(3-hydroxyhexanoyl)-l-homoserine lactone and N-(3-hydroxyoctanoyl)-l-homoserine lactone, were detected in JCM 2778 and DSM 21509 samples. PhzI synthesized all AHLs; however, CsaI could not perform AHL biosynthesis in JCM 2778 and DSM 21509. In both strains, disruption of the phzI caused complete disappearance of phenazine-1-carboxylic acid (PCA) and phenazine-1-carboxamide (PCN) production; however, disruption of csaI did not induce significant changes in PCA and PCN production. Phenazine derivatives produced by JCM 2778 and DSM 21509 under quorum sensing are crucial for the control of the plant pathogenic fungi, Rhizoctonia solani, Fusarium graminearum, and Fusarium nirenbergiae. These results demonstrated that PhzI/PhzR quorum-sensing system play an important role in production of phenazine derivatives and biocontrol activity.

Effects of Marine Sand on the Microbial Degradation of Biodegradable Plastics in Seawater and Biofilm Communities that Formed on Plastic Surfaces

Four types of biodegradable plastics were evaluated for their biodegradability in seawater collected at Ajigaura coast, Japan, in the presence or absence of marine sand. One of the plastics, poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH), showed a degree of biodegradation in a seawater sample, and the addition of marine sand markedly accelerated its biodegradation. The addition of marine sand did not affect the bacterial composition of the biofilm that formed on PHBH, and the family Rhodobacteraceae, which was predicted to contribute to the degradation of PHBH, was dominant in biofilm communities regardless of the addition of marine sand. Marine sand may serve as a bacterial source, resulting in the accelerated degradation of PHBH.

Comparative genome analysis reveals the presence of multiple quorum-sensing systems in plant pathogenic bacterium, Erwinia rhapontici

We present the complete genome sequences of 3 Erwinia rhapontici strains, MAFF 311153, 311154, and 311155. These chromosome sequences contained variety types of luxI/luxR gene pair involved in acylhomoserine lactone biosynthesis and reception. Large-scale insertion sequence was observed in the indigenous plasmid of MAFF 311154 and contained eraI3/eraR3 gene pair that make possible to produce acylhomoserine lactone.

Genetic and functional diversity of PsyI/PsyR quorum-sensing system in the Pseudomonas syringae complex

Strains belonging to the Pseudomonas syringae complex often possess quorum-sensing systems that comprise N-acyl-l-homoserine lactone (AHL) synthases (PsyI) and AHL receptors (PsyR). Here, we investigated the diversity of PsyI/PsyR quorum-sensing systems in 630 strains of the P. syringae complex. AHL production was observed in most strains of Pseudomonas amygdali and Pseudomonas meliae, and a few strains of Pseudomonas coronafaciens and P. syringae. The DNA sequences of psyIR and their upstream and downstream regions were categorized into eight types. P. amygdali pv. myricae, Pseudomonas savastanoi, and P. syringae pv. solidagae, maculicola, broussonetiae, and tomato encoded psyI, but did not produce detectable amounts of AHL. In P. savastanoi, an amino acid substitution (R27S) in PsyI caused defective AHL production. The psyI gene of P. syringae pv. tomato was converted to pseudogenes by frameshift mutations. Escherichia coli harboring psyI genes from P. amygdali pv. myricae, P. syringae pv. solidagae and broussonetiae showed high levels of AHL production. Forced expression of functional psyR restored AHL production in P. amygdali pv. myricae and P. syringae pv. solidagae. In conclusion, our study indicates that the PsyI/PsyR quorum-sensing systems in P. syringae strains are genetically and functionally diverse, with diversity being linked to phylogenetic and pathovar classifications.

Detection of Culturable Bacteria from Tomato Seeds on Media Semi-selective for the Canker Pathogen

Culturable bacteria were isolated from tomato seeds using media selective for the canker pathogen Clavibacter michiganensis subsp. michiganensis. Clustering analysis (>99% identity) revealed the presence of 16 operational taxonomic units (OTUs) among isolates detected on semi-selective media. Three OTUs belonged to the phylum Actinobacteria, including those of Micrococcus and Dermacoccus, and 13 OTUs belonged to the phylum Firmicutes, including Bacillus and related genera. These Gram-positive endophytic bacteria have the potential to provide false-positive results in seed health tests using media considered semi-selective for the cancer pathogen.

Comparative Genome Analysis Reveals Differences in Biocontrol Efficacy According to Each Individual Isolate Belonging to Rhizospheric Fluorescent Pseudomonads

Biocontrol fluorescent pseudomonads produce a number of antibiotic organic compounds, including 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, and phenazine. We previously classified rhizospheric fluorescent pseudomonads harboring antibiotic biosynthetic gene clusters into 10 operational taxonomic units (OTUs). In the present study, we report the complete genome sequences of selected strains from these OTUs. The genetic diversity of antibiotic biosynthetic gene clusters and their surrounding sequences correlated with the OTU classification. In comparisons of the biocontrol activity and distribution of antibiotic biosynthetic gene clusters, we found that the pyrrolnitrin biosynthetic gene cluster more effectively controlled the growth of Rhizoctonia solani.

Diversity of Antibiotic Biosynthesis Gene-possessing Rhizospheric Fluorescent Pseudomonads in Japan and Their Biocontrol Efficacy

More than 3,000 isolates of fluorescent pseudomonads have been collected from plant roots in Japan and screened for the presence of antibiotic-synthesizing genes. In total, 927 hydrogen cyanide (HCN)-, 47 2,4-diacetylphloroglucinol (PHL)-, 6 pyoluteorin (PLT)-, 14 pyrrolnitrin (PRN)-, and 8 phenazine (PHZ)-producing isolates have been detected. A cluster analysis (≥99% identity) identified 10 operational taxonomic units (OTUs) in antibiotic biosynthesis gene-possessing pseudomonads. OTU HLR (PHL, PLT, and PRN) contained four antibiotics: HCN, PHL, PLT, and PRN, while OTU RZ (PRN and PHZ) contained three: HCN, PRN, and PHZ. OTU H1, H2, H3, H4, H5, H6, and H7 (PHL1-7) contained two antibiotics: HCN and PHL, while OTU H8 (PHL8) contained one: PHL. Isolates belonging to OTU HLR and RZ suppressed damping-off disease in cabbage seedlings caused by Rhizoctonia solani. Effective strains belonging to OTU HLR and RZ were related to Pseudomonas protegens and Pseudomonas chlororaphis, respectively. Antibiotic biosynthesis gene-possessing fluorescent pseudomonads are distributed among different geographical sites in Japan and plant species.

Genetic and Biochemical Diversity for N-acylhomoserine Lactone Biosynthesis in the Plant Pathogen Pectobacterium carotovorum subsp. carotovorum

The plant pathogen Pectobacterium carotovorum subsp. carotovorum (Pcc) regulates the expression of virulence factors by N-acylhomoserine lactone (AHL)-mediated quorum sensing. The LuxI family protein, ExpI, catalyzes AHL biosynthesis in Pcc. The structure of the predominant AHL produced by ExpI differs among Pcc strains, which may be divided into two quorum-sensing classes (QS classes) based on the AHL produced. In the present study, AHL produced by 282 Pcc strains were extracted and identified by LC-MS/MS. Seventy Pcc strains produced N-(3-oxooctanoyl)-l-homoserine lactone (3-oxo-C8-HSL) as the predominant AHL and were categorized into QS class I. Two hundred Pcc strains produced N-(3-oxohexanoyl)-l-homoserine lactone (3-oxo-C6-HSL) as the predominant AHL, and were categorized into QS class II-1. Twelve Pcc strains produced only small amounts of 3-oxo-C6-HSL, and were categorized into QS class II-2. The phylogenetic analysis revealed that the amino acid sequences of ExpI may be divided into two major clades (I and II). The Pcc strains categorized into ExpI clades I and II entirely matched QS classes I and II, respectively. A multiple alignment analysis demonstrated that only 6 amino acid substitutions were observed among ExpI from QS classes II-1 and II-2. Furthermore, many amino acid substitutions between QS classes I and II were concentrated at the C-terminal region. These amino acid substitutions are assumed to cause significant reductions in 3-oxo-C6-HSL in QS class II-2 or affect the substrate specificity of ExpI between QS classes I and II.

Distribution and Genetic Diversity of Genes Involved in Quorum Sensing and Prodigiosin Biosynthesis in the Complete Genome Sequences of Serratia marcescens

Quorum sensing is a cell density-dependent regulation of gene expression. N-acyl-l-homoserine lactone (AHL) is a major quorum-sensing signaling molecule in gram-negative bacteria and synthesized by the LuxI family protein. The genus Serratia is known as a producer of the red pigment, prodigiosin, whose biosynthesis is dependent on the pig gene cluster. Some Serratia strains regulate prodigiosin production via AHL-mediated quorum sensing, whereas there is red-pigmented Serratia strains without quorum-sensing system. In addition, nonpigmented Serratia marcescens, which does not produce prodigiosin, has also been isolated from natural and clinical environments. In this study, we aim to reveal the distribution and genetic diversity of quorum-sensing genes and pig gene cluster in the complete genome sequences of S. marcescens. We previously demonstrated that S. marcescens AS-1 regulates the production of prodigiosin via AHL-mediated quorum sensing. We sequenced the genomes of AS-1 and compared with the complete genomes of AS-1 and the other 34 strains of S. marcescens. The luxI homolog was present on 25 complete genome sequences. The deduced amino acid sequences of the luxI homolog were divided into three phylogenetic classes. In contrast, the pig gene cluster was present in the genome of seven S. marcescens strains and only two strains, AS-1 and N4-5 contained both the luxI homolog and pig gene cluster in their genome. It is therefore assumed that prodigiosin production and its regulation by quorum sensing are not essential for the life cycle of S. marcescens.

N-Acylhomoserine lactone-mediated quorum sensing regulates biofilm structure in Methylobacterium populi P-1M, an isolate from a pink-pigmented household biofilm

Numerous gram-negative bacteria have quorum-sensing systems and produce AHL as a quorum-sensing signal molecule. In this study, we demonstrated that Methylobacterium populi P-1M, an isolate from a pink-pigmented household biofilm, produced two AHLs, C14:1-HSL as a predominant product and 3OHC14-HSL as a minor product. The complete genome sequence of M. populi P-1M revealed the presence of genes that are predicted to encode an AHL synthase (mpoI) and AHL receptor (mpoR). M. populi P-1M formed a pellicle-like biofilm, which had a flat surface and was easily removable. In contrast, biofilms formed by mpoI and/or mpoR deletion mutants had a wavy surface structure and strongly adhered to the glass tube. When C14:1-HSL was added to the mpoI mutant culture, the biofilm structure resembled that of the wild-type strain. These results demonstrated that the structure and adhesion strength of M. populi P-1M biofilms are determined in part by AHL-mediated quorum sensing.

Abbreviations: AHL: N-acyl-l-homoserine lactone; C14:1-HSL: N-tetradecenoyl-l-homoserine lactone; 3OHC14-HSL: N-(3-hydroxytetradecanoyl)-l-homoserine lactone; SAM: S-adenosyl-l-methionine; ACP: acyl-acyl carrier protein; EPS: extracellular polysaccharide; DMSO: dimethyl sulfoxide

Biofilm Formation and Degradation of Commercially Available Biodegradable Plastic Films by Bacterial Consortiums in Freshwater Environments

We investigated biofilm formation on biodegradable plastics in freshwater samples. Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH) was covered by a biofilm after an incubation in freshwater samples. A next generation sequencing analysis of the bacterial communities of biofilms that formed on PHBH films revealed the dominance of the order Burkholderiales. Furthermore, Acidovorax and Undibacterium were the predominant genera in most biofilms. Twenty-five out of 28 PHBH-degrading isolates were assigned to the genus Acidovorax, while the other three were assigned to the genera Undibacterium and Chitinimonas. These results demonstrated that the order Burkholderiales in biofilms functions as a degrader of PHBH films.

Molecular Characterization of the Bacterial Community in Biofilms for Degradation of Poly(3-Hydroxybutyrate-co-3-Hydroxyhexanoate) Films in Seawater

Microplastics are fragmented pieces of plastic in marine environments, and have become a serious environmental issue. However, the dynamics of the biodegradation of plastic in marine environments have not yet been elucidated in detail. Polyhydroxyalkanoates (PHAs) are biodegradable polymers that are synthesized by a wide range of microorganisms. One of the PHA derivatives, poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH) has flexible material properties and a low melting temperature. After an incubation in seawater samples, a significant amount of biofilms were observed on the surfaces of PHBH films, and some PHBH films were mostly or partially degraded. In the biofilms that formed on the surfaces of unbroken PHBH films, the most dominant operational taxonomic units (OTUs) showed high similarity with the genus Glaciecola in the family Alteromonadaceae. On the other hand, the dominant OTUs in the biofilms that formed on the surfaces of broken PHBH films were assigned to the families Rhodobacteraceae, Rhodospirillaceae, and Oceanospirillaceae, and the genus Glaciecola mostly disappeared. The bacterial community in the biofilms on PHBH films was assumed to have dynamically changed according to the progression of degradation. Approximately 50 colonies were isolated from the biofilm samples that formed on the PHBH films and their PHBH-degrading activities were assessed. Two out of three PHBH-degrading isolates showed high similarities to Glaciecola lipolytica and Aestuariibacter halophilus in the family Alteromonadaceae. These results suggest that bacterial strains belonging to the family Alteromonadaceae function as the principal PHBH-degrading bacteria in these biofilms.

Genomic Analysis of Two Phylogenetically Distinct Nitrospira Species Reveals Their Genomic Plasticity and Functional Diversity

The genus Nitrospira represents a dominant group of nitrite-oxidizing bacteria in natural and engineered ecosystems. This genus is phylogenetically divided into six lineages, for which vast phylogenetic and functional diversity has been revealed by recent molecular ecophysiological analyses. However, the genetic basis underlying these phenotypic differences remains largely unknown because of the lack of genome sequences representing their diversity. To gain a more comprehensive understanding of Nitrospira, we performed genomic comparisons between two Nitrospira strains (ND1 and NJ1 belonging to lineages I and II, respectively) previously isolated from activated sludge. In addition, the genomes of these strains were systematically compared with previously reported six Nitrospira genomes to reveal their similarity and presence/absence of several functional genes/operons. Comparisons of Nitrospira genomes indicated that their genomic diversity reflects phenotypic differences and versatile nitrogen metabolisms. Although most genes involved in key metabolic pathways were conserved between strains ND1 and NJ1, assimilatory nitrite reduction pathways of the two Nitrospira strains were different. In addition, the genomes of both strains contain a phylogenetically different urease locus and we confirmed their ureolytic activity. During gene annotation of strain NJ1, we found a gene cluster encoding a quorum-sensing system. From the enriched supernatant of strain NJ1, we successfully identified seven types of acyl-homoserine lactones with a range of C10–C14. In addition, the genome of strain NJ1 lacks genes relevant to flagella and the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated genes) systems, whereas most nitrifying bacteria including strain ND1 possess these genomic elements. These findings enhance our understanding of genomic plasticity and functional diversity among members of the genus Nitrospira.

Complete Genome Sequence of Pseudomonas chlororaphis subsp. aurantiaca Reveals a Triplicate Quorum-Sensing Mechanism for Regulation of Phenazine Production

Pseudomonas chlororaphis subsp. aurantiaca StFRB508 regulates phenazine production through N-acyl-l-homoserine lactone (AHL)-mediated quorum sensing. Two sets of AHL-synthase and AHL-receptor genes, phzI/phzR and aurI/aurR, have been identified from the incomplete draft genome of StFRB508. In the present study, the complete genome of StFRB508, comprising a single chromosome of 6,997,933 bp, was sequenced. The complete genome sequence revealed the presence of a third quorum-sensing gene set, designated as csaI/csaR. An LC-MS/MS analysis revealed that StFRB508 produced six types of AHLs, with the most important AHL being N-(3-hydroxyhexanoyl)-l-homoserine lactone (3-OH-C6-HSL). PhzI mainly catalyzed the biosynthesis of 3-OH-C6-HSL, while AurI and CsaI catalyzed that of N-hexanoyl-l-homoserine lactone and N-(3-oxohexanoyl)-l-homoserine lactone, respectively. A mutation in phzI decreased phenazine production, whereas that in aurI or csaI did not. A phzI aurI csaI triple mutant (508ΔPACI) did not produce phenazine. Phenazine production by 508ΔPACI was stimulated by exogenous AHLs and 3-OH-C6-HSL exerted the strongest effects on phenazine production at the lowest concentration tested (0.1 μM). The plant protection efficacy of 508ΔPACI against an oomycete pathogen was lower than that of wild-type StFRB508. These results demonstrate that the triplicate quorum-sensing system plays an important role in phenazine production by and the biocontrol activity of StFRB508.

Characterization of N-Acylhomoserine Lactones Produced by Bacteria Isolated from Industrial Cooling Water Systems

The cooling water systems are used to remove heat generated in the various industries. Biofouling of the cooling water systems causes blocking of condenser pipes and the heat exchanger tubes. In many Gram-negative bacteria, N-acylhomoserine lactone (AHL) are used as quorum-sensing signal molecule and associated with biofilm formation. To investigate the relationship between quorum sensing and biofouling in the cooling water system, we isolated a total of 192 bacterial strains from the five cooling water systems, and screened for AHL production. Seven isolates stimulated AHL-mediated purple pigment production in AHL reporter strain Chromobacterium violaceum CV026 or VIR07. Based on their 16S rRNA gene sequences, AHL-producing isolates were assigned to Aeromonas hydrophila, Lysobacter sp., Methylobacterium oryzae, and Bosea massiliensis. To the best of our knowledge, B. massiliensis and Lysobacter sp. have not been reported as AHL-producing species in the previous researches. AHLs extracted from the culture supernatants of B. massiliensis and Lysobacter sp. were identified by liquid chromatography-mass spectrometry. AHLs produced by B. massiliensis were assigned as N-hexanoyl-l-homoserine lactone (C6-HSL), N-(3-oxohexanoyl)-l-homoserine lactone (3-oxo-C6-HSL), and N-(3-oxooctanoyl)-l-homoserine lactone (3-oxo-C8-HSL). AHLs produced by Lysobacter sp. were assigned as N-decanoyl-l-homoserine lactone (C10-HSL) and N-(3-oxodecanoyl)-l-homoserine lactone (3-oxo-C10-HSL). This is the first report of identification of AHLs produced by B. massiliensis and Lysobacter sp. isolated from the cooling water system.

Pseudomonas aeruginosa quorum-sensing signaling molecule N-3-oxododecanoyl homoserine lactone induces matrix metalloproteinase 9 expression via the AP1 pathway in rat fibroblasts

Quorum sensing is a cell-to-cell communication mechanism, which is responsible for regulating a number of bacterial virulence factors and biofilm maturation and therefore plays an important role for establishing wound infection. Quorum-sensing signals may induce inflammation and predispose wounds to infection by Pseudomonas aeruginosa; however, the interaction has not been well investigated. We examined the effects of the P. aeruginosa las quorum-sensing signal, N-3-oxo-dodecanoyl homoserine lactone (3OC12-HSL), on matrix metalloproteinase (MMP) 9 expression in Rat-1 fibroblasts. 3OC12-HSL upregulated the expression of the MMP9 gene bearing an activator protein-1 (AP-1) binding site in the promoter region. We further investigated the mechanism underlying this effect. c-Fos gene expression increased rapidly after exposure to 3OC12-HSL, and nuclear translocation of c-Fos protein was observed; both effects were reduced by pretreatment with an AP-1 inhibitor. These results suggest that 3OC12-HSL can alter MMP9 gene expression in fibroblasts via the AP-1 signaling pathway.

Characterization of a novel thermostable N-acylhomoserine lactonase from the thermophilic bacterium Thermaerobacter marianensis

Thermaerobacter marianensis is an extremely thermophilic bacterium, which was isolated from the Mariana Trench, with an optimal growth temperature of approximately 75 °C. N-Acylhomoserine lactone (AHL) is a quorum-sensing signal molecule used by many gram-negative bacteria. Here, we report the identification of an AHL-degrading gene homolog (designated aiiT) in the genome of T. marianensis JCM 10246. AiiT has 59.7%, 21.2%, and 11.2% identity to AhlS from Solibacillus silvestris, AiiA from Bacillus cereus, and AidC from Chryseobacterium sp., respectively. Homologs of aiiT were also found in Thermaerobacter nagasakiensis, T. composti, and T. subterraneus. A purified AiiT-maltose binding fusion showed high AHL-degrading activity against N-hexanoyl-L-homoserine lactone, N-octanoyl-L-homoserine lactone, and N-decanoyl-L-homoserine lactone at temperatures ranging from 40 to 80 °C. HPLC analysis revealed that AiiT functions as an AHL-lactonase that catalyzes AHL ring opening by hydrolyzing lactones. AiiT displayed maximal activity at high temperatures (60-80 °C) and showed higher thermostability than other AHL lactonases.

The ppuI-rsaL-ppuR quorum-sensing system regulates cellular motility, pectate lyase activity, and virulence in potato opportunistic pathogen Pseudomonas sp. StFLB209

Pseudomonas sp. StFLB209 was isolated from potato leaf as an N-acylhomoserine lactone (AHL)-producing bacterium and showed a close phylogenetic relationship with P. cichorii, a known plant pathogen. Although there are no reports of potato disease caused by pseudomonads in Japan, StFLB209 was pathogenic to potato leaf. In this study, we reveal the complete genome sequence of StFLB209, and show that the strain possesses a ppuI-rsaL-ppuR quorum-sensing system, the sequence of which shares a high similarity with that of Pseudomonas putida. Disruption of ppuI results in a loss of AHL production as well as remarkable reduction in motility. StFLB209 possesses strong pectate lyase activity and causes maceration on potato tuber and leaf, which was slightly reduced in the ppuI mutant. These results suggest that the quorum-sensing system is well conserved between StFLB209 and P. putida and that the system is essential for motility, full pectate lyase activity, and virulence in StFLB209.

Evaluation of intraspecies interactions in biofilm formation by Methylobacterium species isolated from pink-pigmented household biofilms

Concern regarding household biofilms has grown due to their widespread existence and potential to threaten human health by serving as pathogen reservoirs. Previous studies identified Methylobacterium as one of the dominant genera found in household biofilms. In the present study, we examined the mechanisms underlying biofilm formation by using the bacterial consortium found in household pink slime. A clone library analysis revealed that Methylobacterium was the predominant genus in household pink slime. In addition, 16 out of 21 pink-pigmented bacterial isolates were assigned to the genus Methylobacterium. Although all of the Methylobacterium isolates formed low-level biofilms, the amount of the biofilms formed by Methylobacterium sp. P-1M and P-18S was significantly increased by co-culturing with other Methylobacterium strains that belonged to a specific phylogenetic group. The single-species biofilm was easily washed from the glass surface, whereas the dual-species biofilm strongly adhered after washing. A confocal laser scanning microscopy analysis showed that the dual-species biofilms were significantly thicker and tighter than the single-species biofilms.

Genetic diversity and ecological evaluation of fluorescent pseudomonads isolated from the leaves and roots of potato plants

A total of 828 isolates of fluorescent pseudomonads (FPs) were obtained from the leaves (305 isolates) and roots (523 isolates) of potato plants grown in different geographical locations in Japan, and 16S rRNA gene sequences of 776 isolates were successfully determined by direct PCR sequencing. Clustering analysis (≥99% identity) identified 13 and 26 operational taxonomic units (OTUs) for leaf- and root-associated FPs, respectively, and 29 OTUs were identified in the phytosphere of potato plants. Among them, 7 and 9 OTUs showed a significantly biased distribution to the leaves and roots, respectively. Phylogenetic analysis revealed that 3 dominant OTUs for leaf-associated FPs were grouped in a cluster of leaf-associated pathogens, such as Pseudomonas cichorii and Pseudomonas viridiflava. In contrast, 4 OTUs were located in a cluster of saprophytic pseudomonads. Among them, 3 OTUs showed high similarity to Pseudomonas koreensis and Pseudomonas vancouverensis, both of which have been reported to be beneficial for biological control or plant growth promotion. These data provide key information for efficient surveying and utilization of beneficial FPs in agricultural practices.

Diversity and distribution of N-acylhomoserine lactone (AHL)-degrading activity and AHL-lactonase (AiiM) in genus microbacterium

N-Acylhomoserine lactone (AHL)-degrading enzyme, AiiM, was identified from the potato leaf-associated Microbacterium testaceum StLB037. In this study, we cloned eight aiiM gene homologues from other AHL-degrading Microbacterium strains. The similarity of the chromosomal locus of the aiiM gene is associated with the phylogenetic classification based on 16S rRNA. Degenerate PCR revealed that the aiiM gene was only conserved in AHL-degrading Microbacterium strains, but not in fifteen Microbacterium type strains or two Microbacterium isolates from other plants. These results suggested that the high level of AHL-degrading activity in Microbacterium strains was caused by the aiiM gene encoded on their chromosome.

Complete genome sequence and characterization of the N-acylhomoserine lactone-degrading gene of the potato leaf-associated Solibacillus silvestris

N-Acylhomoserine lactones (AHLs) are used as quorum-sensing signal molecules by many gram-negative bacteria. We have reported that Solibacillus silvestris, which was isolated from the potato leaf, has AHL-degrading activity. To identify the AHL-degrading gene, whole genome sequencing of S. silvestris StLB046 was performed by using pyrosequencing technology. As the result of the BLAST search, one predicted ORF (ahlS) showed slight similarity to AiiA-like AHL lactonase from Bacillus cereus group. Escherichia coli harboring the ahlS-expressing plasmid showed high AHL-degrading activity. The ahlS-cording region was also amplified by PCR from the other potato leaf-associated and AHL-degrading S. silvestris strains. Purified AhlS as a maltose binding fusion protein showed high AHL-degrading activity and catalyzes AHL ring opening by hydrolyzing lactones. In addition, expression of ahlS in plant pathogen Pectobacterium carotovorum subsp. carotovorum attenuated maceration of the potato slices. Our results suggest that AHL-degrading activity of ahlS might perform useful functions such as useful biocontrol agents.

Diversity of culturable chitinolytic bacteria from rhizospheres of agronomic plants in Japan

A total of 100 isolates of chitinolytic bacteria were obtained from the rhizospheres of various agronomic plants, and the 16S rRNA gene sequences of these isolates were determined. Phylogenetic analyses revealed that 81 isolates belonged to the classes Betaproteobacteria (39 isolates) and Gammaproteobacteria (42 isolates). Of the remaining 19 isolates, 16 belonged to the phylum Firmicutes. Clustering analysis identified 6 and 3 operational taxonomic units (OTUs) in Gammaproteobacteria and Betaproteobacteria, respectively, at the genus level. The majority of chitinolytic bacteria in Gammaproteobacteria belonged to the genera Serratia, Stenotrophomonas, and Lysobacter (14, 15, and 7 isolates, respectively) while those in Betaproteobacteria belonged to the genus Mitsuaria (37 isolates). The 16 isolates placed in Firmicutes belonged to 2 genera, Paenibacillus and Bacillus (8 isolates each). The isolates in the remaining OTUs belonged to the genera Erwinia, Aeromonas, Pseudomonas, Achromobacter, Flavobacterium, and Microbacterium, in less abundance. These results showed a wide distribution of culturable chitinolytic bacteria in the rhizospheres of various agronomic plants. Considering the potential antagonistic activity of chitinolytic enzymes against phytopathogenic fungi, which is exhibited by fungal cell wall degradation, the above-mentioned native chitinolytic bacteria in rhizospheres could potentially be utilized for the biological control of soil-borne phytopathogenic fungi.

Isolation and characterization of novel lipases from a metagenomic library of the microbial community in the pitcher fluid of the carnivorous plant Nepenthes hybrida

Members of the genus Nepenthes are carnivorous plants that use the pitfall method of insect capture as a supplementary nutritional source. We extracted metagenomic DNA from the microbial community found in the pitcher fluid of Nepenthes and constructed a plasmid-based metagenomic library. An activity-based screening method enabled the isolation of two lipase genes, lip1 and lip2. Both Lip1 and Lip2 belong to a novel family or subfamily of lipases and show lipase activities in acidic conditions, such as those found in pitcher fluid. This study was conducted under the assumption that the secreted Lip1 and Lip2 were capable of enzymatic activity in the acidic pitcher fluid.

Contribution of quorum sensing to the virulence of Pseudomonas aeruginosa in pressure ulcer infection in rats

The impact of quorum sensing (QS) in in vivo models of infection has been widely investigated, but there are no descriptions for ischemic wound infection. To explore the role of QS in Pseudomonas aeruginosa in the establishment of ischemic wound infection, we challenged a pressure ulcer model in rats with the PAO-1, PAO-1 derivatives ΔlasIΔrhlI and ΔlasRΔrhlR strains, which cannot induce the virulence factor under QS control, thus the reduced tissue destruction was expended in these mutant strains. However unexpectedly, on postwounding day 3, the inflammatory responses in the three groups were similarly severe and the numbers of bacteria in tissue samples did not differ among the three strains. Biofilm formation was immature in QS-deficient strains, defined by the absence of dense bacterial aggregates and extracellular polymeric substance, which was confirmed by scanning electron microscopy. The Pseudomonas aeruginosa QS signal, acylated homoserine lactone, was only quantified from wound samples in the PAO-1 group. The swimming and twitching motilities were significantly enhanced in the ΔlasRΔrhlR group compared with the PAO-1 group in vitro. A significantly larger wound area was correlated with the bacterial motility. The inflammation in the early phase of bacterial challenge to wounds with immature biofilm formation in the QS-deficient strains indicated that the role of QS was more crucial for the chronic phase than for the acute phase of infection. The present findings indicate a difference in the importance of QS in ischemic wound infections compared with other infection models.

The Pseudomonas aeruginosa quorum-sensing signal N-(3-oxododecanoyl) homoserine lactone can accelerate cutaneous wound healing through myofibroblast differentiation in rats

Quorum sensing is a cell density-dependent gene regulation system in bacteria. N-(3-oxododecanoyl) homoserine lactone (3-oxo-C12-HSL) is used in the las quorum-sensing system in Pseudomonas aeruginosa, which is an opportunistic pathogen that causes many human diseases. Although many studies have investigated the sole effects of quorum sensing on several types of mammalian cells, including lung cells, little is known about the effects of quorum sensing on the cells associated with wound healing. To better understand the mechanism of bacterial wound infection, we investigated the effects of 3-oxo-C12-HSL on cells using a rat full-thickness wound-healing model. We found that the wound contraction was significantly increased at 24 h after the administration of 3-oxo-C12-HSL to the surface of granulation tissue. Differentiation of fibroblasts to myofibroblasts was induced in the in vivo wound-healing model and was confirmed in vitro using the rat fibroblastic cell line Rat-1. Cyclooxygenase (Cox)-2 expression was also induced in Rat-1 cells by 3-oxo-C12-HSL. This finding suggested that Cox-2 upregulation may be related to the inflammatory findings in the histological examinations, in which infiltrating polymorphonuclear neutrophils were observed at the wound site. Taken together, these results imply that mammals have a potential defense system against invading pathogens by responding to the presence of 3-oxo-C12-HSL and inducing the differentiation of fibroblasts to myofibroblasts as well as inflammation for accelerating wound healing.

Piecewise affine systems approach to control of biological networks

In terms of a piecewise affine system representation, which is a kind of hybrid system model, this article discusses a series of approaches to modelling, analysing and synthesizing a biological network such as a gene-regulatory network. First, the input assignment problem, the controllable state set problem (CSP) and the input trajectory generation problem are emphasized as control problems to be addressed for biological networks. Subsequently, after the modelling issue on biological networks developed in the systems and control community is briefly explained, the CSP is described in detail with reference to control of the quorum-sensing system in the pathogen Pseudomonas aeruginosa. Finally, an optimal control design method to the quorum-sensing system is proposed as a solution to the input trajectory generation problem.

Secretion of intelectin-1 from malignant pleural mesothelioma into pleural effusion

Background:

Malignant pleural mesothelioma (MPM) is a rare but fatal tumour. Although most MPM patients show pleural effusion at even the early stage, it is hard to diagnose as MPM at the early stage because a sensitive and reliable diagnostic marker for MPM has not been found in plasma or pleural effusion.

Methods:

In this study, we investigated whether intelectin-1 was specifically contained in MPM cells and the pleural effusion of MPM patient by immunohistochemistry, western blotting, and enzyme-linked immunosorbent assay.

Results:

Malignant pleural mesothelioma cell lines, but not lung adenocarcinoma cell lines, secreted intelectin-1. In immunohistochemistry, epithelioid-type MPMs, but neither pleura-invading lung adenocarcinomas nor reactive mesothelial cells near the lung adenocarcinomas, were stained with anti-intelectin antibodies. Pleural effusion of MPM patients contained a higher concentration of intelectin-1 than that of lung cancer patients.

Conclusion:

These results suggest that detection of intelectin-1 may be useful for a differential diagnosis of epithelioid-type MPM in immunohistochemistry and that a high concentration of intelectin-1 in pleural effusion can be used as a new marker for clinical diagnosis of MPM.

Motility and the expression of the flagellin protein FliC are negatively regulated by quorum sensing in Edwardsiella tarda

Edwardsiella tarda is a gram-negative bacterial pathogen of fish and animals. A number of gram-negative bacteria have quorum-sensing systems and produce N-acylhomoserine lactone (AHL) that they use as a quorum-sensing signaling molecule. We have already reported that E. tarda NUF251 produces AHLs and has the AHL-synthase gene, edwI. Inactivation of NUF251 edwI induces expression of an approximately 45 kDa extracellular protein, identified as a flagellin encoded by FliC. Mutation of edwI also changes the motility pattern of NUF251 from a radial expansion pattern to concentric rings. The addition of exogenous AHL was capable of restoring normal motility to NUF251 edwI mutants. These results demonstrate that quorum sensing negatively regulates motility and expression of the FliC protein.

Inhibition of Lux quorum-sensing system by synthetic N-acyl-L-homoserine lactone analogous

In the present study, we investigated the inhibition of the Lux quorum-sensing system by N-acyl cyclopentylamine (Cn-CPA). The Lux quorum-sensing system regulates luminescence gene expression in Vibrio fischeri. We have already reported on the synthesis of Cn-CPA and their abilities as inhibitors of the quorum-sensing systems in Pseudomonas aeruginosa and Serratia marcescens. In the case of Pseudomonas aeruginosa (Las and Rhl quorum-sensing system) and Serratia marcescens (Spn quorum-sensing system), specific Cn-CPA with a particular acyl chain length showed the strongest inhibitory effect. In the case of the Lux quorum-sensing system, it was found that several kinds of Cn-CPA with a range from C5 to C10 showed similar strong inhibitory effects. Moreover, the inhibitory effect of Cn-CPA on the Lux quorum-sensing system was stronger than that of halogenated furanone, a natural quorum-sensing inhibitor.

The function of SpnR and the inhibitory effects by halogenated furanone on quorum sensing in Serratia marcescens AS-1

By secretion and detection of a series of signaling molecules, bacteria are able to coordinate gene expression as a community, to regulate a variety of important phenotypes, from virulence factor production to biofilm formation to symbiosis related behaviours such as bioluminescence. This widespread signaling mechanism is called quorum sensing. There are several quorum sensing systems described in Serratia. Serratia marcescens AS-1, isolated from soil, had the LuxI/LuxR homologues called SpnI/SpnR. S. marcescens AS-1 produced two kinds of N-acyl-L-homoserine lactones, N-hexanoyl-L-homoserine lactone and N-(3-oxohexanoyl)-L-homoserine lactone as signal molecules, which involved in quorum sensing to control the gene expression in response to increased cell density. By gene replacement method, the spnR mutant was constructed, named S. marcescens AS-1R. SpnR acted as a negative regulator for the production of prodigiosin, swarming motility and biofilm formation, which were regulated by quorum sensing. Halogenated furanone, known as a natural inhibitor of quorum sensing, could effectively inhibit the quorum sensing of S. marcescens AS-1 but without interrupting AHL-SpnR interaction. All results will be helpful to understand the mechanisms of halogenated furanone inhibition on quorum sensing and the potential application of halogenated furanone in effectively preventing infection disease caused by Serratia strains.