Multi-omics analysis of miRNA-mediated intestinal microflora changes in crucian carp Carassius auratus infected with Rahnella aquatilis

Infection by an emerging bacterial pathogen Rahnella aquatilis caused enteritis and septicemia in fish. However, the molecular pathogenesis of enteritis induced by R. aquatilis infection and its interacting mechanism of the intestinal microflora associated with microRNA (miRNA) immune regulation in crucian carp Carassius auratus are still unclear. In this study, C. auratus intraperitoneally injected with R. aquatilis KCL-5 was used as an experimental animal model, and the intestinal pathological changes, microflora, and differentially expressed miRNAs (DEMs) were investigated by multi-omics analysis. The significant changes in histopathological features, apoptotic cells, and enzyme activities (e.g., lysozyme (LYS), alkaline phosphatase (AKP), alanine aminotransferase (ALT), aspartate transaminase (AST), and glutathione peroxidase (GSH-Px)) in the intestine were examined after infection. Diversity and composition analysis of the intestinal microflora clearly demonstrated four dominant bacteria: Proteobacteria, Fusobacteria, Bacteroidetes, and Firmicutes. A total of 87 DEMs were significantly screened, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes were mainly involved in the regulation of lipid, glutathione, cytosine, and purine metabolism, which participated in the local immune response through the intestinal immune network for IgA production, lysosome, and Toll-like receptor (TLR) pathways. Moreover, the expression levels of 11 target genes (e.g., TLR3, MyD88, NF-κB, TGF-β, TNF-α, MHC II, IL-22, LysC, F2, F5, and C3) related to inflammation and immunity were verified by qRT-PCR detection. The correlation analysis indicated that the abundance of intestinal Firmicutes and Proteobacteria was significantly associated with the high local expression of miR-203/NF-κB, miR-129/TNF-α, and miR-205/TGF-β. These findings will help to elucidate the molecular regulation mechanism of the intestinal microflora, inflammation, and immune response-mediated miRNA-target gene axis in cyprinid fish.

Gallic and ferulic acids suppress proteolytic activities and volatile trimethylamine production in the food-borne spoiler Rahnella aquatilis KM05

BACKGROUND

Rahnella aquatilis is a recognised microbial threat that alters the sensory properties of seafood. The high frequency with which R. aquatilis is isolated from fish has prompted a search for alternative preservatives. In the present study, in vitro and fish-based ecosystem (raw salmon-based medium) approaches were used to validate the antimicrobial effects of gallic (GA) and ferulic (FA) acids against R. aquatilis KM05. The results were compared with data describing the response of KM05 to sodium benzoate. Bioinformatics data of the whole genome were used to analyse the potential for fish spoilage by KM05 in detail, and the results revealed the main physiological characteristics that underlie reduced seafood quality.

RESULTS

In the KM05 genome, the most abundantly enriched Gene Ontology terms were 'metabolic process', 'organic substance metabolic process' and 'cellular process'. Through an evaluation of the Pfam annotations, 15 annotations were found to be directly involved in the proteolytic activity of KM05. Peptidase_M20 was the most abundantly represented (abundance value of 14060). Proteins representing the CutC family (abundance value of 427) indicated the potential for KM05 degradation of trimethyl-amine-N-oxide. Subinhibitory concentrations of GA and FA suppressed the proteolytic activities of KM05 both in vitro and in RS medium by an average of 33-45%. These results were confirmed by quantitative real-time PCR experiments, which also showed that the expression levels of genes involved in proteolytic activities and volatile trimethylamine production were also decreased.

CONCLUSION

Phenolic compounds can be used as potential food additives for preventing quality deterioration of fish products. © 2023 Society of Chemical Industry.

Single-cell transcriptome, phagocytic activity and immunohistochemical analysis of crucian carp (Carassius auratus) in response to Rahnella aquatilis infection

In teleost fish, kidney is an important immune and hematopoietic organ with multiple physiological functions. However, the immune cells and cellular markers of kidney require further elucidation in crucian carp (C. auratus). Here we report on the single-cell transcriptional landscape in posterior kidney, immunohistochemical and phagocytic features of C. auratus with R. aquatilis infection. The results showed that a total of 18 cell populations were identified for the main immune cells such as monocytes/macrophages (Mo/Mφ), dendritic cells (DCs), B cells, T cells, granulocytes and hematopoietic progenitor cells (HPCs). Pseudo-time trajectory analysis was reconstructed for the immune cells using Monocle2 to obtain additional insights into their developmental lineage relationships. In the detected tissues (liver, spleen, kidney, intestine, skin, and gills) of infected fish exhibited positive immunohistochemical staining with prepared for antibody to R. aquatilis. Apoptotic cells were fluorescently demonstrated by TUNEL assay, and bacterial phagocytic activity were observed for neutrophils and Mo/Mφ cells, respectively. Moreover, a similar up-ward/down-ward expression trend of the selected immune and inflammatory genes was found in the kidney against R. aquatilis infection, which were significantly involved in TLR/NLR, ECM adhesion, phago-lysosome, apoptosis, complement and coagulation pathways. To our knowledge, this is the first report on the detailed characterization of immune cells and host-R. aquatilis interaction, which will contribute to understanding on the biology of renal immune cells and repertoire of potential markers in cyprinid fish species.

Uptake of Selenite by Rahnella aquatilis HX2 Involves the Aquaporin AqpZ and Na+/H+ Antiporter NhaA

Microbial transformation of selenite [Se(IV)] to elemental selenium nanoparticles (SeNPs) is known to be an important process for removing toxic soluble selenium (Se) oxyanions and recovery of Se from the environment as valuable nanoparticles. However, the mechanism of selenite uptake by microorganisms, the first step through which Se exerts its cellular function, remains not well studied. In this study, the effects of selenite concentration, time, pH, metabolic inhibitors, and anionic analogues on selenite uptake in Rahnella aquatilis HX2 were investigated. Selenite uptake by R. aquatilis HX2 was concentration- and time-dependent, and its transport activity was significantly dependent on pH. In addition, selenite uptake in R. aquatilis HX2 was significantly inhibited by the aquaporin inhibitor AgNO₃ and sulfite (SO₃^2-), and partially inhibited by carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and 2,4-dinitrophenol (2,4-DNP) treatments. Three mutants with in-frame deletions of aqpZ, glpF, and nhaA genes were constructed. The transport assay showed that the water channel protein AqpZ, and not GlpF, was a key channel of selenite uptake by R. aquatilis HX2, and sulfite and selenite had a common uptake pathway. In addition, the Na⁺/H⁺ antiporter NhaA is also involved in selenite uptake in R. aquatilis HX2.

First report on the characterization of pathogenic Rahnella aquatilis KCL-5 from crucian carp: Revealed by genomic and proteomic analyses

Rahnella aquatilis is an important pathogen of several aquatic organisms and is found widely distributed in the freshwater, soil, fish and human clinical samples. Our previously published study reported a novel pathogenic R. aquatilis strain KCL-5 to crucian carp (Carassius auratus). To further investigate the characteristics and pathogenesis caused by R. aquatilis, we here report on the pathological changes, bacterial genomic and proteomic analyses of strain KCL-5. Significantly pathological changes in liver, intestine, spleen and gills were observed in infected fish. The genome consists of one circular chromosome 5,062,299 bp with 52.02% GC content and two plasmids (506,827 bp, 52.16%; 173,433 bp, 50.00%) and predicted 5,653 genes, 77 tRNAs and 22 rRNAs. Some virulence factors were characterized, including outer membrane protein, haemolysin, RTX toxin, chemotaxis and T3SS secretion system. Antimicrobial resistance genes such as EmrAB-TolC, MexABC-OpmB and RosAB efflux pump were found in strain KCL-5. KEGG analysis showed that mainly functional modules were ABC transporters, biosynthesis of amino acids, two-component system, quorum sensing, flagellum assembly and chemotaxis, in which most of them were identified by using 2-DE/MS analyses. To our knowledge, this was first report on the molecular characteristics of R. aquatilis by multi-omics approaches, which will provide insights into the pathogenic mechanism of R. aquatilis infection in fish.

The complete genome sequence of Rahnella aquatilis ZF7 reveals potential beneficial properties and stress tolerance capabilities

Rahnella aquatilis ZF7 is a plant beneficial strain isolated from Sakura tree soil with potential for biocontrol. Here, we present the complete genome sequence of R. aquatilis ZF7, which consists of one 4.49 Mb circular chromosome and a 54-kb plasmid named pRAZF7. Phylogenetic analyses revealed that R. aquatilis ZF7 is much similar to the strains Rahnella sp. Y9602 and R. aquatilis HX2 than others evaluated. In this study, multiple genes encoding functions that likely contribute to plant growth promotion, biocontrol and stress tolerance were identified by comparative genome analyses, including IAA production, phosphate solubilization, antibiotic resistance and formation of Se nanoparticles (SeNPs). In addition, these functions were also confirmed by in vitro experiments. Considering its ability to form SeNPs, strain R. aquatilis ZF7 will contribute to nano-agriculture. Overall, the features of R. aquatilis ZF7 make it a high potential and competitive strain in biocontrol, and the genome data will help further studies on the mechanisms of plant growth promotion and biocontrol.

The arbuscular mycorrhizal fungus Rhizophagus irregularis MUCL 43194 induces the gene expression of citrate synthase in the tricarboxylic acid cycle of the phosphate-solubilizing bacterium Rahnella aquatilis HX2

An increasing number of studies have demonstrated that arbuscular mycorrhizal fungi can cooperate with other soil microorganisms, e.g., bacteria, which develop near or on the surface of the extraradical hyphae where they perform multiple functions. However, the mechanisms involved in this privileged relationship are still poorly known. In the present study, we investigated how the arbuscular mycorrhizal fungus Rhizophagus irregularis MUCL 43194 influences the three pace-making enzymes (i.e., citrate synthase, isocitrate dehydrogenase, and α-oxoglutarate dehydrogenase) of the tricarboxylic acid (TCA) cycle in the phosphate-solubilizing bacterium Rahnella aquatilis HX2. The study was conducted under strict in vitro culture conditions and analysis made at the transcriptional level. Results showed that R. irregularis induced the expression of the gene-encoding citrate synthase (gltA), the pace-making enzyme involved in the first step of the TCA cycle, in R. aquatilis at all time points of observation (i.e., 1, 6, 12, 24, 48, and 72 h). The expression of the gene-encoding isocitrate dehydrogenase (icd) significantly decreased at 6, 12, 24, 48, and 72 h and the expression of the gene-encoding α-oxoglutarate dehydrogenase E1 component (kgdhc) significantly increased at 1, 6, and 48 h. The above results suggested that R. irregularis may influence the level of adenosine triphosphate production in R. aquatilis and thus the metabolism of the bacterium by stimulating the expression of gltA involved in the TCA cycle. Our results suggest a fine-tuned dialog between R. irregularis MUCL 43194 and R. aquatilis HX2 and emphasize the complexity of the interactions that might take place at the hyphal surface of arbuscular mycorrhizal fungi hosting communities of microbes.

First report of Rahnella aquatilis infection in crucian carp Carassius auratus in China

Rahnella aquatilis infection is rare in aquaculture. Here, a Gram-negative rod-shaped bacterium was isolated from diseased crucian carp Carassius auratus in Xuzhou City, Jiangsu Province, eastern China. The isolate was tentatively named strain KCL-5, and subsequently identified as R. aquatilis by biochemical properties and molecular techniques. The results showed that the isolate KCL-5 was most closely related to the type strain ATCC33071 (= DSM4594) of R. aquatilis, which shared 99.67, 96.26 and 99.58% nucleotide sequence identities for 16S rDNA, gyrB and toxin yhaV genes, respectively. Experimental challenges were conducted which demonstrated pathogenicity of the isolate in crucian carp. Antimicrobial susceptibility testing showed that the isolated strain was susceptible to piperacillin, gentamicin, kanamycin, nalidixic acid, norfloxacin, ofloxacin, azithromycin and erythromycin. To our knowledge, this is the first report on R. aquatilis infection in crucian carp, and the first evidence of pathogenicity in fish.

Inoculation of Lens culinaris with Pb-resistant bacteria shows potential for phytostabilization

Phytoremediation comprises a set of plant and microbe-based technologies for remediation of soil heavy metal contamination. In this work, four Pb-resistant bacteria (Agrobacterium tumefaciens, Rahnella aquatilis, and two Pseudomonas sp.) were selected among a collection of isolates from root nodule of Lens culinaris. They had a high degree of bioaccumulation ability in nutrient medium containing 2 mM Pb, and the maximum Pb accumulation of whole cell was found after 48-h incubation. These Pb-resistant bacteria synthesized plant growth promoting substances such as indole acetic acid and siderophore. The presence of the Pb resistance genes (pbrA) in these bacteria has been confirmed by PCR. L. culinaris cultivated in two experimental soils with different levels of contamination showed that Pb contamination affected plant growth; therefore, it's co-inoculation with the consortium of Pb-resistant bacteria improved plant biomass. The present study demonstrated that lentil accumulated Pb primarily in their roots and poorly in their shoots; in addition, it's co-inoculation in moderately Pb-contaminated soil induced a reduction in Pb accumulation in roots and shoots by 22 and 80 %, respectively. Whereas in highly Pb-contaminated soil, we registered a diminution in concentration of Pb in shoots (66 %) and an augmentation in roots (21 %). The contamination of soil by Pb caused an oxidative stress in lentil plant, inducing modulation in antioxidant enzymes activities, essentially in superoxide dismutase (SOD) and peroxidase (GPOX) activities which were more pronounced in lentil cultivated in highly Pb-contaminated soil, in addition, co-inoculation enhanced these activities, suggesting the protective role of enzymatic antioxidant against Pb-induced plant stress.Thus, the present study demonstrated that co-inoculation of lentil with A. tumefaciens, R. aquatilis, and Pseudomonas sp. formed a symbiotic system useful for phytostabilization of highly and moderately Pb-contaminated soils.

Disruption of gene pqqA or pqqB reduces plant growth promotion activity and biocontrol of crown gall disease by Rahnella aquatilis HX2

Rahnella aquatilis strain HX2 has the ability to promote maize growth and suppress sunflower crown gall disease caused by Agrobacterium vitis, A. tumefaciens, and A. rhizogenes. Pyrroloquinoline quinone (PQQ), a cofactor of aldose and alcohol dehydrogenases, is required for the synthesis of an antibacterial substance, gluconic acid, by HX2. Mutants of HX2 unable to produce PQQ were obtained by in-frame deletion of either the pqqA or pqqB gene. In this study, we report the independent functions of pqqA and pqqB genes in relation to PQQ synthesis. Interestingly, both the pqqA and pqqB mutants of R. aquatilis eliminated the ability of strain HX2 to produce antibacterial substance, which in turn, reduced the effectiveness of the strain for biological control of sunflower crown gall disease. The mutation also resulted in decreased mineral phosphate solubilization by HX2, which reduced the efficacy of this strain as a biological fertilizer. These functions were restored by complementation with the wild-type pqq gene cluster. Additionally, the phenotypes of HX2 derivatives, including colony morphology, growth dynamic, and pH change of culture medium were impacted to different extents. Our findings suggested that pqqA and pqqB genes individually play important functions in PQQ biosynthesis and are required for antibacterial activity and phosphorous solubilization. These traits are essential for R. aquatilis efficacy as a biological control and plant growth promoting strain. This study enhances our fundamental understanding of the biosynthesis of an environmentally significant cofactor produced by a promising biocontrol and biological fertilizer strain.

Enhancement of Cd phytoextraction by two Amaranthus species with endophytic Rahnella sp. JN27

Microbe-assisted phytoextraction shows a potential for the remediation of metal-contaminated soils. The aim of this study was to isolate, characterize, and evaluate the potential of endophytic bacteria in improving plant growth and metal uptake by Cd-hyperaccumulators-Amaranthus hypochondriacus and Amaranthus mangostanus. An endophytic bacterial strain JN27 isolated from roots of Zea mays displayed high tolerance and mobilization to Cd, and was identified as Rahnella sp. based on 16S rDNA sequencing. The strain also exhibited multiple plant growth beneficial features including the production of indole-3-acetic acid, siderophore, 1-aminocyclopropane-1-carboxylic acid deaminase and solubilization of insoluble phosphate. Subsequently, a pot trial was performed to elucidate the effects of inoculation with JN27 on plant growth and Cd uptake by A. hypochondriacus, A. mangostanus, Solanum nigrum and Z. mays grown in soils with different levels of Cd (25, 50, 100 mg Cd kg(-1)). The results revealed that inoculation with JN27 significantly increased the biomasses of all the tested plants and the Cd concentrations of all the tested plants except Z. mays in both above-ground and root tissues. Moreover, strain JN27 could successfully re-colonized in rhizosphere soils of all the tested plants and root interior of A. hypochondriacus and Z. mays. The present results indicated that the symbiont of A. hypochondriacus (or A. mangostanus) and strain JN27 can effectively improve the Cd uptake by plants and would be a new strategy in microbe-assisted phytoextraction for metal-contaminated soils.

Characterization of endophytic Rahnella sp. JN6 from Polygonum pubescens and its potential in promoting growth and Cd, Pb, Zn uptake by Brassica napus

Microbe-assisted phytoremediation has been considered as a promising measure for the remediation of heavy metal-polluted soils. In this study, a metal-tolerance and plant growth-promoting endophytic bacterium JN6 was firstly isolated from roots of Mn-hyperaccumulator Polygonum pubescens grown in metal-contaminated soil and identified as Rahnella sp. based on 16S rDNA gene sequence analysis. Strain JN6 showed very high Cd, Pb and Zn tolerance and effectively solubilized CdCO(3), PbCO(3) and Zn(3)(PO(4))(2) in culture solution. The isolate produced plant growth-promoting substances such as indole-3-acetic acid, siderophore, 1-aminocyclopropane-1-carboxylic deaminase, and also solubilized inorganic phosphate. Based upon its ability in metal tolerance and solubilization, the isolate JN6 was further studied for its effects on the growth and accumulation of Cd, Pb and Zn in Brassica napus (rape) by pot experiments. Rape plants inoculated with the isolate JN6 had significantly higher dry weights, concentrations and uptake of Cd, Pb and Zn in both above-ground and root tissues than those without inoculation grown in soils amended with Cd (25 mg kg(-1)), Pb (200 mg kg(-1)) or Zn (200 mg kg(-1)). The isolate also showed a high level of colonization in tissue interior of rapes. The present results demonstrated that Rahnella sp. JN6 is a valuable microorganism, which can cost-effectively improve the efficiency of phytoremediation in soils contaminated by Cd, Pb and Zn.

Draft genome sequence of Rahnella aquatilis strain HX2, a plant growth-promoting rhizobacterium isolated from vineyard soil in Beijing, China

Rahnella aquatilis strain HX2 is a plant growth-promoting, disease-suppressive rhizobacterium that was isolated from a vineyard soil in Beijing, China. Here, we report the genome sequence of this strain, which provides a valuable resource for future research examining the mechanisms of traits associated with plant growth promotion and biocontrol.

A novel 5-enolpyruvylshikimate-3-phosphate synthase from Rahnella aquatilis with significantly reduced glyphosate sensitivity

The 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; EC 2.5.1.19) is a key enzyme in the shikimate pathway for the production of aromatic amino acids and chorismate-derived secondary metabolites in plants, fungi, and microorganisms. It is also the target of the broad-spectrum herbicide glyphosate. Natural glyphosate resistance is generally thought to occur within microorganisms in a strong selective pressure condition. Rahnella aquatilis strain GR20, an antagonist against pathogenic agrobacterial strains of grape crown gall, was isolated from the rhizosphere of grape in glyphosate-contaminated vineyards. A novel gene encoding EPSPS was identified from the isolated bacterium by complementation of an Escherichia coli auxotrophic aroA mutant. The EPSPS, named AroA(R. aquatilis), was expressed and purified from E. coli, and key kinetic values were determined. The full-length enzyme exhibited higher tolerance to glyphosate than the E. coli EPSPS (AroA(E. coli)), while retaining high affinity for the substrate phosphoenolpyruvate. Transgenic plants of AroA(R. aquatilis) were also observed to be more resistant to glyphosate at a concentration of 5 mM than that of AroA(E. coli). To probe the sites contributing to increased tolerance to glyphosate, mutant R. aquatilis EPSPS enzymes were produced with the c-strand of subdomain 3 and the f-strand of subdomain 5 (Thr38Lys, Arg40Val, Arg222Gln, Ser224Val, Ile225Val, and Gln226Lys) substituted by the corresponding region of the E. coli EPSPS. The mutant enzyme exhibited greater sensitivity to glyphosate than the wild type R. aquatilis EPSPS with little change of affinity for its first substrate, shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP). The effect of the residues on subdomain 5 on glyphosate resistance was more obvious.

Cold-adapted and rhizosphere-competent strain of Rahnella sp. with broad-spectrum plant growth-promotion potential

A phosphate-solubilizing bacterial strain isolated from Hippophae rhamnoides rhizosphere was identified as Rahnella sp. based on its phenotypic features and 16S rRNA gene sequence. The bacterial strain showed the growth characteristics of a cold-adapted psychrotroph, with the multiple plant growth-promoting traits of inorganic and organic phosphate solubilization, 1-aminocyclopropane-1- carboxylate-deaminase activity, ammonia generation, and siderophore production. The strain also produced indole- 3-acetic acid, indole-3-acetaldehyde, indole-3-acetamide, indole-3-acetonitrile, indole-3-lactic acid, and indole-3- pyruvic acid in tryptophan-supplemented nutrient broth. Gluconic, citric and isocitric acids were the major organic acids detected during tricalcium phosphate solubilization. A rifampicin-resistant mutant of the strain exhibited high rhizosphere competence without disturbance to the resident microbial populations in pea rhizosphere. Seed bacterization with a charcoal-based inoculum significantly increased growth in barley, chickpea, pea, and maize under the controlled environment. Microplot testing of the inoculum at two different locations in pea also showed significant increase in growth and yield. The attributes of coldtolerance, high rhizosphere competence, and broad-spectrum plant growth-promoting activity exhibited the potential of Rahnella sp. BIHB 783 for increasing agriculture productivity.

Mutations that disrupt either the pqq or the gdh gene of Rahnella aquatilis abolish the production of an antibacterial substance and result in reduced biological control of grapevine crown gall

Rahnella aquatilis HX2, a biocontrol agent for grapevine crown gall caused by Agrobacterium vitis, produces an antibacterial substance that inhibits the growth of A. vitis in vitro. In this study, we show that MH15 and MH16, two Tn5-induced mutants of HX2, have lost their abilities to inhibit A. vitis and have reduced biocontrol activities; they grow in logarithmic phase at a rate similar to that of the wild type and have single Tn5 insertions. They are also impaired in producing pyrroloquinoline quinone (PQQ) or glucose dehydrogenase (GDH). Complementation of MH15 and MH16 with cosmid clones of CP465 and CP104 from an HX2 DNA library restored the antibiosis, biocontrol, and PQQ or GDH production phenotypes. A 6.7-kb BamHI fragment from CP465 that fully restored the MH15-affected phenotypes was cloned and sequenced. Sequence analysis of the mutated DNA region resulted in the identification of seven open reading frames (ORFs), six of which share significant homology with PQQ-synthesizing genes in other bacteria, designated pqqA through pqqF. Meanwhile, A 5.5-kb PstI fragment from CP104 fully complemented the MH16 mutant and contained a single ORF highly similar to that of genes coding for GDHs. An in-frame gdh deletion mutant has the same phenotypes as the Tn5 mutant of MH16. Complementation of both deletion and Tn5 gdh mutants restored the affected phenotypes to wild-type levels. Our results suggest that an antibacterial substance plays a role in biocontrol of A. vitis by HX2.

Isolation and characterization of pHW15, a small cryptic plasmid from Rahnella genomospecies 2

A small cryptic plasmid designated pHW15 was isolated from Rahnella genomospecies 2 WMR15 and its complete nucleotide sequence was determined. The plasmid contained 3002 bp with a G+C content of 47.4%. The origin of replication was identified by deletion analysis as a region of about 600 bp. This region had an identity of 70% to the replication origin of the ColE1 plasmid at the nucleotide level. Sequence analysis revealed the typical elements: RNA I, RNA II and their corresponding promoters, a sequence allowing hybridisation of RNA II to the DNA and favouring processing by RNaseH, a single-strand initiation determinant (ssi) that allows initiation of lagging-strand synthesis, and a terH sequence required for termination of lagging-strand synthesis. The plasmid contained three expressed open reading frames, one of which showed homology to a ColE1 plasmid-encoded protein. Furthermore, a multimer resolution site was identified by sequence analysis. Its deletion resulted in formation of plasmid multimers during growth leading to an increased plasmid loss rate.

Pseudomonas, the dominant polycyclic aromatic hydrocarbon-degrading bacteria isolated from Antarctic soils and the role of large plasmids in horizontal gene transfer

Twenty-two polycyclic aromatic hydrocarbon (PAH)-degrading bacterial strains were isolated from Antarctic soils with naphthalene or phenanthrene as a sole carbon source, while no degrader was obtained from an unpolluted sampling site. Phylogenetic analysis showed that all belonged to the genus Pseudomonas except one that was identified as the genus of Rahnella. Some of them were closely related to previously reported cold-tolerant species, while some were separated in deeply rooted branches and represent new strains. All these strains showed a high efficiency to degrade naphthalene at 4 degrees C, and some additionally degraded phenanthrene. Using degenerate primers and polymerase chain reaction (PCR) amplification, ndo gene encoding naphthalene dioxygenase (NDO) was detected from all the isolates. Phylogenetic analysis grouped these genes into two clusters which shared 94% similarity to each other, and showed about 97% similarity within a cluster. However, no obvious difference was observed with mesophilic ndo genes; this indicates that the host cell is pivotal in cold adaptation. In addition, the mismatch between 16S rRNA and NDO phylogenetic trees strongly indicates horizontal gene transfer among these isolates and may have happened in situ. Further, Southern hybridization and plasmid curing confirmed that ndo genes were located on a large self-transmissible plasmid, which can be transferred to a mesophilic strains. The transconjugants acquired the ability to utilize naphthalene and phenanthrene. Results of this article imply that Pseudomonas plays an important role in PAH biodegradation in Antarctic soils, and the related genes might be originally transferred from outside Antarctica and spread among indigenous species.

[Biological activity of native and modified lipopolysaccharides of Rahnella aquatilis]

Modified lipopolysaccharide (LPS) preparations: dephosphorylated and N,O-dcacylated ones of six strains of Rahnella aquatilis have been obtained. It has been shown that the modified LPS, in contrast to native ones, have lost completely their toxicity and pathogenicity. This can evidence for the participation of both acyl, and phosphoryl groups in biological activity of LPS of R. aquatilis.

-1 frameshifting at a CGA AAG hexanucleotide site is required for transposition of insertion sequence IS1222

The discovery of programmed -1 frameshifting at the hexanucleotide shift site CGA_AAG, in addition to the classical X_XXY_YYZ heptanucleotide shift sequences, prompted a search for instances among eubacterial insertion sequence elements. IS1222 has a CGA_AAG shift site. A genetic analysis revealed that frameshifting at this site is required for transposition.

Molecular characterization of the growth phase-dependent expression of the lsrA gene, encoding levansucrase of Rahnella aquatilis

Expression of the lsrA gene from Rahnella aquatilis, encoding levansucrase, is tightly regulated by the growth phase of the host cell; low-level expression was observed in the early phase of cell growth, but expression was significantly stimulated in the late phase. Northern blot analysis revealed that regulation occurred at the level of transcription. The promoter region was identified by primer extension analysis. Two opposite genetic elements that participate in the regulation of lsrA expression were identified upstream of the lsrA gene: the lsrS gene and the lsrR region. The lsrS gene encodes a protein consisting of 70 amino acid residues (M(r), 8,075), which positively activated lsrA expression approximately 20-fold in a growth phase-dependent fashion. The cis-acting lsrR region, which repressed lsrA expression about 10-fold, was further narrowed to two DNA regions by deletion analysis. The concerted action of two opposite regulatory functions resulted in the growth phase-dependent activation of gene expression in Escherichia coli independent of the stationary sigma factor sigma(S).

Biochemical-genetic characterization of the chromosomally encoded extended-spectrum class A beta-lactamase from Rahnella aquatilis

From whole-cell DNA of a clinical isolate of the enterobacterial species Rahnella aquatilis, a beta-lactamase gene was cloned that encoded a chromosomally encoded Ambler class A enzyme, RAHN-1. RAHN-1, with a pI of 7.2, shares 76, 73, and 71% amino acid identity with the extended-spectrum beta-lactamase of chromosomal origin from Serratia fonticola and with the plasmid-mediated beta-lactamases CTX-M-2 and CTX-M-1, respectively. The hydrolysis spectrum of the clavulanic acid-inhibited RAHN-1 was expanded to cephalosporins such as cefuroxime, cefotaxime, and ceftriaxone, but not to ceftazidime. Its expression was not inducible.

Molecular cloning of a gene encoding the thermoactive levansucrase from Rrahnella aquatilis and its growth phase-dependent expression in Eescherichia coli

A levansucrase gene (lsrA) from Rahnella aquatilis ATCC33071 was isolated from a genomic library and the nucleotide sequence of the lsrA structural gene was determined. lsrA is composed of 1248 bp and encodes 415 amino acid residues with a calculated molecular mass of 45.9 kDa. Although the amino acid sequence of lsrA gene showed good conservation with the sequences of reported levansucrases and of the conserved regions thought to be implicated in the enzyme activity, comparison of the deduced amino acid sequences certified the dissimilarity of the proteins from Gram-negative and Gram-positive bacteria. The lsrA gene was expressed from its own promoter in Escherichia coli in an active form. The lsrA expression in E. coli-pRL1CPR was affected by the growth phase of cells: it was repressed in the early phase of growth, but was significantly stimulated during the entrance of cells into the late phase of growth. The growth-phase-dependent fashion of lsrA expression was altered in a constitutive-like fashion by the deletion of an upstream region of lsrA (pNd137), suggesting that the growth-phase dependent expression of lsrA was mediated by the deleted upstream region.