Ecological genomics of marine Roseobacters

Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode proteins involved in the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered: vir-related genes encoding a type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft Roseobacter genomes include those for carbon monoxide oxidation, dimethylsulfoniopropionate demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation.

Transcriptional regulation ofSalmonella entericaserovar Typhimurium genes by bile

DNA microarrays and two-dimensional (2-D) gel electrophoresis were utilized to analyze the global effect of bile on transcription and protein synthesis in Salmonella enterica serovar Typhimurium. Two bile-regulated proteins, YciF and PagC, were identified by 2-D gel electrophoresis and mass spectrometry fingerprinting. The operon yciGFE-katN demonstrated increased transcriptional activity in the presence of bile. While this operon has previously been shown to be RpoS-regulated, data from this study suggested that yciGFE-katN is regulated by bile independent of RpoS. The PhoP-PhoQ-regulated PagC is decreased in the presence of bile. Characterization of the untranslated leader of pagC demonstrated that a 97-bp region is necessary for the bile-mediated repression of this promoter. Analysis of data from the DNA microarray revealed an effect of bile on important global mechanistic pathways in S. enterica serovar Typhimurium. Genes involved in type III secretion-mediated invasion of epithelial cells demonstrated an overall repression of transcription in the presence of bile, corroborating previously reported data from this laboratory [Infect. Immun. 68 (2000) 6763]. In addition, bile-mediated transcriptional repression of genes involved in flagellar biosynthesis and motility was observed. These data further demonstrate that bile is an important environmental signal sensed by Salmonella spp. and that bile plays a role in regulating bacterial gene expression in multiple virulence-associated pathways.

Bacterial community associated with Pfiesteria-like dinoflagellate cultures

Dinoflagellates (Eukaryota; Alveolata; Dinophyceae) are single-cell eukaryotic microorganisms implicated in many toxic outbreaks in the marine and estuarine environment. Co-existing with dinoflagellate communities are bacterial assemblages that undergo changes in species composition, compete for nutrients and produce bioactive compounds, including toxins. As part of an investigation to understand the role of the bacteria in dinoflagellate physiology and toxigenesis, we have characterized the bacterial community associated with laboratory cultures of four 'Pfiesteria-like' dinoflagellates isolated from 1997 fish killing events in Chesapeake Bay. A polymerase chain reaction with oligonucleotide primers specific to prokaryotic 16S rDNA gene sequences was used to characterize the total bacterial population, including culturable and non-culturable species, as well as possible endosymbiotic bacteria. The results indicate a diverse group of over 30 bacteria species co-existing in the dinoflagellate cultures. The broad phylogenetic types of dinoflagellate-associated bacteria were generally similar, although not identical, to those bacterial types found in association with other harmful algal species. Dinoflagellates were made axenic, and the culturable bacteria were added back to determine the contribution of the bacteria to dinoflagellate growth. Confocal scanning laser fluorescence microscopy with 16S rDNA probes was used to demonstrate a physical association of a subset of the bacteria and the dinoflagellate cells. These data point to a key component in the bacterial community being species in the marine alpha-proteobacteria group, most closely associated with the alpha-3 or SAR83 cluster.

Serum immunoglobulin response and protection from homologous challenge by Proteus mirabilis in a mouse model of ascending urinary tract infection

We tested the hypothesis that experimental Proteus mirabilis urinary tract infection in mice would protect against homologous bladder rechallenge. Despite production of serum immunoglobulin G (IgG) and IgM (median titers of 1:320 and 1:80, respectively), vaccinated (infected and antibiotic-cured) mice did not show a decrease in mortality upon rechallenge; the survivors experienced only modest protection from infection (mean log(10) number of CFU of P. mirabilis Nal(r) HI4320 per milliliter or gram in vaccinated mice versus sham-vaccinated mice: urine, 100-fold less [3.5 versus 5.5; P = 0.13]; bladder, 100-fold less [3.1 versus 5.1; P = 0.066]; kidneys, 40-fold less [2.7 versus 4.3; P = 0.016]). Western blots using protein from the wild-type strain and isogenic mutants demonstrated antibody responses to MR/P and PMF fimbriae and flagella. There was no correlation between serum IgG or IgM levels and protection from mortality or infection. There was a trend toward elevated serum IgA titers and protection from subsequent challenge (P >/= 0.09), although only a few mice developed significant serum IgA levels. We conclude that prior infection with P. mirabilis does not protect significantly against homologous challenge.

ZapA, the IgA-degrading metalloprotease of Proteus mirabilis, is a virulence factor expressed specifically in swarmer cells

The IgA-degrading metalloprotease, ZapA, of the urinary tract pathogen Proteus mirabilis is co-ordinately expressed along with other proteins and virulence factors during swarmer cell differentiation. In this communication, we have used zapA to monitor IgA protease expression during the differentiation of vegetative swimmer cells to fully differentiated swarmer cells. Northern blot analysis of wild-type cells and beta-galactosidase measurements using a zapA:lacZ fusion strain indicate that zapA is fully expressed only in differentiated swarmer cells. Moreover, the expression of zapA on nutrient agar medium is co-ordinately regulated in concert with the cycles of cellular differentiation, swarm migration and consolidation that produce the bull's-eye colonies typically associated with P. mirabilis. ZapA activity is not required for swarmer cell differentiation or swarming behaviour, as ZapA- strains produce wild-type colony patterns. ZapA- strains fail to degrade IgA and show decreased survival compared with the wild-type cells during infection in a mouse model of ascending urinary tract infection (UTI). These data underscore the importance of the P. mirabilis IgA-degrading metalloprotease in UTI. Analysis of the nucleotide sequences adjacent to zapA reveals four additional genes, zapE, zapB, zapC and zapD, which appear to possess functions required for ZapA activity and IgA proteolysis. Based on homology to other known proteins, these genes encode a second metalloprotease, ZapE, as well as a ZapA-specific ABC transporter system (ZapB, ZapC and ZapD). A model describing the function and interaction of each of these five proteins in the degradation of host IgA during UTI is presented.

Genomic rearrangements in the flagellin genes of Proteus mirabilis

Molecular analyses have revealed that Proteus mirabilis possesses two genes, flaA and flaB, that are homologous to each other and to flagellin genes of many other species. Both swimmer and swarmer cells transcribe flaA, but not flaB. FlaA- mutants are non-motile and do not differentiate showing the essential role of flaA in swarmer cell differentiation and behaviour. At a low frequency, motile, differentiation-proficient revertants have been found in FlaA-populations. These revertants produce an antigenically and biochemically distinct flagellin protein. The revertant flagellin is the result of a genetic fusion between highly homologous regions of flaA and flaB that places the active flaA promoter and the 5' coding region of flaA adjacent to previously silent regions of flaB generating a hybrid flagellin protein. Analysis of the flaA-flaB region of two such revertants reveals that a portion of this locus has undergone a rearrangement and deletion event that is unique to each revertant. Using a polymerase chain reaction (PCR) to amplify the falA-flaB locus from wild-type swimmer cells, swarmer cells and cells obtained after urinary tract infection, we uncover at least six general classes of rearrangements between flaA and flaB. Each class of rearrangement occurs within one of nine domains of homology between flaA and flaB. Rearrangement of flaA and flaB results in a hybrid flagellin protein of nearly identical size and biochemical properties, suggesting a concerted mechanism may be involved in this process. The data also reveal that the frequency and distribution of flaAB rearrangements is predicted on environmental conditions. Thus, rearrangement between flaA and flaB may be a significant virulence component of P. mirabilis in urinary tract infections.

Characterization of Proteus mirabilis precocious swarming mutants: identification of rsbA, encoding a regulator of swarming behavior

Proteus mirabilis swarming behavior is characterized by the development of concentric rings of growth that are formed as cyclic events of swarmer cell differentiation, swarming migration, and cellular differentiation are repeated during colony translocation across a surface. This cycle produces the bull's-eye colony often associated with cultures of P. mirabilis. How the cells communicate with one another to coordinate these perfectly synchronized rings is presently unknown. We report here the identification of a genetic locus that, when mutated, results in a precocious swarming phenotype. These mutants are defective in the temporal control of swarming migration and start swarming ca. 60 min sooner than wild-type cells. Unlike the wild type, precocious swarming mutants are also constitutive swarmer cells and swarm on minimal agar medium. The defects were found to be localized to a 5.4-kb locus on the P. mirabilis genome encoding RsbA (regulator of swarming behavior) and the P. mirabilis homologs to RcsB and RcsC. RsbA is homologous to membrane sensor histidine kinases of the two-component family of regulatory proteins, suggesting that RsbA may function as a sensor of environmental conditions required to initiate swarming migration. Introduction of a rsbA mutation back into the wild type via allelic-exchange mutagenesis reconstructed the precocious swarming phenotype, which could be complemented in trans by a plasmid-borne copy of rsbA. Overexpression of RsbA in wild-type cells resulted in precocious swarming, suggesting that RsbA may have both positive and negative functions in regulating swarming migration. A possible model to describe the role of RsbA in swarming migration is discussed.

Construction of a flagellum-negative mutant of Proteus mirabilis: effect on internalization by human renal epithelial cells and virulence in a mouse model of ascending urinary tract infection

To examine the role of flagella in pathogenesis of urinary tract infection caused by Proteus mirabilis, we constructed a nonmotile, nonswarming flagellum mutant of strain WPM111 (an hpmA hemolysin mutant of strain BA6163, chosen because of its lack of in vitro cytotoxicity in renal epithelial cell internalization studies). A nonpolar mutation was introduced into the flaD gene, which encodes the flagellar cap protein. This mutation does not affect the synthesis of flagellin but rather prevents the assembly of an intact flagellar filament. In in vitro assays, the genetically characterized nonmotile mutant was found to be internalized by cultured human renal proximal tubular epithelial cells in numbers less than 1% of those of the flagellated parent strain. Internalization of the nonmotile mutant was increased significantly (14- to 21-fold) by centrifugation onto the monolayer. To assess virulence in vivo, CBA mice were challenged transurethrally with 10(7) CFU of P. mirabilis BA6163 (wild type) (n = 16), WPM111 (hpmA mutant) (n = 46), or BB2401 (hmpA flaD mutant) (n = 46). Differences in quantitative cultures between the parent strain and the hemolysin-negative mutant were not significant. However, the hpmA flaD mutant was recovered in numbers approximately 100-fold lower than those of the hmpA mutant or the wild-type parent strain and thus was clearly attenuated. We conclude that while hemolysin does not significantly influence virulence, flagella contribute significantly to the ability of P. mirabilis to colonize the urinary tract and cause acute pyelonephritis in an experimental model of ascending urinary tract infection.

Molecular analysis of a metalloprotease from Proteus mirabilis

Proteus mirabilis is known for its ability to differentiate from swimmer to swarmer cells, a process crucial for the pathogenesis of these bacteria during urinary tract infections. Among the many virulence factors produced during swarmer cell differentiation is an extracellular metalloprotease. A cosmid containing a large fragment of P. mirabilis chromosomal DNA was obtained by measuring protease expression in recombinant Escherichia coli. The recombinant and native enzymes were purified to over 95% homogeneity from culture supernatants by use of phenyl-Sepharose affinity chromatography and found to be identical. The activity of the 55-kDa enzyme was stimulated by divalent cations (Ca2+ > Mg2+) and inhibited by a chelator of these cations. The enzyme possesses substrate specificity for both serum and secretory forms of immunoglobulin A1 (IgA1) and IgA2 as well as IgG and, unlike classic IgA proteases, digested to completion both human and mouse IgA. Following subcloning, a 5-kb DNA fragment encoding recombinant protease activity was identified by insertional mutagenesis with Tn5. Four open reading frames were identified within this 5-kb region by limited nucleotide sequence analysis of DNA flanking the transposon. The nucleotide and deduced amino acid sequences of the metalloprotease structural gene (zapA) were obtained. Computerized homology studies revealed that the P. mirabilis metalloprotein is a member of the serralysin family of proteases and may be part of an operon comprising genes encoding an ATP-dependent ABC transporter in addition to the metalloprotease. The relevance of the metalloprotease to swarmer cell differentiation and pathogenicity is discussed.

Swarming and pathogenicity of Proteus mirabilis in the urinary tract

Proteus mirabilis is best known for its pattern of swarming differentiation on agar plates, as well as for its association with the development of renal stones in patients with urinary tract infection. Urease and flagella appear to contribute most significantly to virulence, with fimbriae playing a more subtle role, whereas hemolysin does not appear to contribute significantly to pathogenesis.

Genetic analysis of Proteus mirabilis mutants defective in swarmer cell elongation

Swarmer cell differentiation is a complex process involving the activity of many gene products. In this report, we characterized the genetic locus of Tn5 insertion in each of 12 mutants defective in swarmer cell elongation. The mutations fell into four categories affecting either flagellar biosynthesis or energetics, lipopolysaccharide and cell wall biosynthesis, cellular division, or proteolysis of peptides.

Expression of multiple flagellin-encoding genes of Proteus mirabilis

The overproduction of flagella is a distinguishing characteristic of Proteus mirabilis swarmer cell differentiation. The synthesis of flagellin, the principal protein composing the flagellar filament, is coordinately regulated as part of a larger regulon of genes whose expression is a prerequisite in urinary pathogenesis. In this report, the regulation of expression of the flaA locus, comprising flaA and flaB, two tandemly linked and nearly identical copies of flagellin-encoding genes, is examined. Transcriptional expression studies reveal that flaA, but not flaB, is expressed by wild-type cells, and flaA transcription increases eightfold during differentiation. The flaA transcriptional start site for both swimmer and swarmer cells was determined to be located at a guanine, 8 bases downstream of the flaA sigma 28 promoter. FlaA- mutants are nonmotile and undifferentiated and do not synthesize flagellin, while FlaB- mutants are wild type, thus verifying that FlaA is the sole flagellin produced by wild-type cells and that flaB is silent. FlaA- mutants frequently revert to a Mot+ phenotype that is antigenically distinct from that of wild-type cells. Southern blot analysis of the flaA Mot+ revertants reveals a deletion of between 2 and 7kb in the flaA locus. Biochemical analyses of revertant flagellin indicate major changes in protein size and composition but conservation of the first 28 N-terminal residues. The result of this process is to produce an antigenically distinct flagellum that may be significant in ensuring the survival of P. mirabilis during pathogenesis.

Sequence and genetic analysis of multiple flagellin-encoding genes from Proteus mirabilis

Surface-induced overproduction of flagellin is one of the hallmarks of Proteus mirabilis swarmer cell differentiation. In this study, we analyzed the nucleotide (nt) and amino acid (aa) sequences, and expression of the P. mirabilis flagellin-encoding gene (fliC) region. The nt sequence analysis of a 3567-bp region reveals three ORFs, each with homology to known Escherichia coli flagellar genes. The first ORF corresponds to fliD, the gene encoding the flagellar filament capping protein, FliD (HAP2). The second and third ORFs are highly homologous to each other and to fliC genes from many other Gram- bacteria. To distinguish between the two alleles, we have designated these genes fliC1 and fliC2. Sequences highly homologous to promoter sites for the alternate sigma factor of RNA polymerase, sigma 28, are found 5' to the start of each gene. Additionally, both fliC1 and fliC2 have a conserved direct tandem repeat (DTR) sequence upstream from the sigma 28 promoter that may have functional significance in the transcriptional control of fliC expression during swarmer cell differentiation. Both FliC1 and FliC2 were produced in E. coli, but only FliC1 could complement FliC- mutants of E. coli. Southern hybridization data indicate the presence of fliC1 and fliC2 in six distinct P. mirabilis strains, indicating that multiple flagellin-encoding genes are common in P. mirabilis. Hybridization data also suggest the presence of a third flagellin-encoding gene, fliC3, in all isolates. The possible significance of multiple fliC in swarmer cell differentiation is discussed.

Transposon mutagenesis in Proteus mirabilis

A technique of transposon mutagenesis involving the use of Tn5 on a suicide plasmid was developed for Proteus mirabilis. Analysis of the resulting exconjugants indicated that Tn5 transposed in P. mirabilis at a frequency of ca. 4.5 x 10(-6) per recipient cell. The resulting mutants were stable and retained the transposon-encoded antibiotic resistance when incubated for several generations under nonselective conditions. The frequency of auxotrophic mutants in the population, as well as DNA-DNA hybridizaiton to transposon sequences, confirmed that the insertion of the transposon was random and the Proteus chromosome did not contain significant insertional hot spots of transposition. Approximately 35% of the mutants analyzed possessed plasmid-acquired ampicillin resistance, although no extrachromosomal plasmid DNA was found. In these mutants, insertion of the Tn5 element and a part or all of the plasmid had occurred. Application of this technique to the study of swarmer cell differentiation in P. mirabilis is discussed.

Proteus mirabilis mutants defective in swarmer cell differentiation and multicellular behavior

Proteus mirabilis is a dimorphic bacterium which exists in liquid cultures as a 1.5- to 2.0-microns motile swimmer cell possessing 6 to 10 peritrichous flagella. When swimmer cells are placed on a surface, they differentiate by a combination of events that ultimately produce a swarmer cell. Unlike the swimmer cell, the polyploid swarmer cell is 60 to 80 microns long and possesses hundreds to thousands of surface-induced flagella. These features, combined with multicellular behavior, allow the swarmer cells to move over a surface in a process called swarming. Transposon Tn5 was used to produce P. mirabilis mutants defective in wild-type swarming motility. Two general classes of mutants were found to be defective in swarming. The first class was composed of null mutants that were completely devoid of swarming motility. The majority of nonswarming mutations were the result of defects in the synthesis of flagella or in the ability to rotate the flagella. The remaining nonswarming mutants produced flagella but were defective in surface-induced elongation. Strains in the second general class of mutants, which made up more than 65% of all defects in swarming were motile but were defective in the control and coordination of multicellular swarming. Analysis of consolidation zones produced by such crippled mutants suggested that this pleiotropic phenotype was caused by a defect in the regulation of multicellular behavior. A possible mechanism controlling the cyclic process of differentiation and dediferentiation involved in the swarming behavior of P. mirabilis is discussed.

Sequence analysis of the agrA gene encoding beta-agarase from Pseudomonas atlantica

The nucleotide sequence of the agrA gene encoding an extracellular beta-agarase of Pseudomonas atlantica was determined. An open reading frame of 1,515 nucleotides which corresponded to agrA was found. The nucleotide sequence predicts a primary translation product of 504 amino acids and Mr 57,486. Comparison of the deduced amino acid sequences of beta-agarase from P. atlantica and the extracellular beta-agarase from Streptomyces coelicolor A3(2) suggests that these proteins share several domains in common.

Regulation of lateral flagella gene transcription in Vibrio parahaemolyticus

Two distinctly different organelles of locomotion are produced by Vibrio parahaemolyticus. The polar flagellum is responsible for motility in a liquid environment (swimming), and the lateral flagella enable the bacteria to move over surfaces (swarming). Synthesis of lateral flagella occurs when V. parahaemolyticus is grown on agar media but not when it is grown in liquid media. We used lux (luminescence gene) fusions to conveniently and sensitively analyze the factors which influence transcription of lateral flagella genes (laf). Transposon mini-Mu lux was used to mutagenize V. parahaemolyticus and to generate laf::lux transcriptional fusions. Mutants with insertions of mini-Mu lux in laf genes were defective in the swarming phenotype and produced light when the bacteria were propagated on agar media, but not when cells were grown in liquid media. Thus, surface-dependent expression of lateral flagella synthesis is controlled by regulation of transcription. Such fusion strains were also used to further define the environmental conditions which induce laf gene expression. Cultivation on media solidified by gelling agents other than agar also induced light production in fusion strains, as did growth on a variety of hydrophilic membrane filters suspended over liquid media. Growth at an air-surface interface was not necessary for expression since embedding the fusion strains in agar was also effective. Furthermore, induction of laf gene transcription could also be accomplished by increasing the viscosity of the liquid medium by the addition of a high-molecular-weight polymer such as polyvinylpyrrolidone. Increase in luminescence of the fusion strains was detected within 30 min of initiation of the inducing circumstance, and reversal of induction, e.g., by dilution of the viscous medium, resulted in a rapid decline in the rate of increase in luminescence. Conditions that induced luminescence in the fusion strains also induced the synthesis of lateral flagella in wild-type V. parahaemolyticus. The growth environment of the genes, and it appears that the signal that triggers laf expression is physical rather than chemical in nature. Possibilities for a sensing mechanism are discussed.

Transposon mutagenesis of marine Vibrio spp

Coliphage P1 was used to transduce derivatives of transposons Tn5 and mini-Mu into marine Vibrio spp. Transposon Tn5 encoding tetracycline resistance (Tn5-132) was used to isolate mutants of Vibrio harveyi defective in genes for bioluminescence (lux). Insertion of transposon Tn5-132 into the lux gene region was demonstrated by intraspecific transduction with phage hv-1 and by Southern blot hybridization. Transposon mini-Mu, modified to specify tetracycline resistance, was employed to mutagenize genes for lateral flagella synthesis of Vibrio parahaemolyticus. Mini-Mu contains the lacZ structural gene, and transposition results in transcriptional fusion of Vibrio genes with the transposon lacZ gene. Thus, in these fusions, lacZ expression was proportional to the level of transcription of the target gene. Regulation of lateral flagella gene expression was studied in vivo by measuring beta-galactosidase activity, and conditions which activate transcription of these genes were identified. A method for gene cloning with transposon-induced mutations is discussed.

Bacterial bioluminescence: isolation and expression of the luciferase genes from Vibrio harveyi

Genes for the luciferase enzyme of Vibrio harveyi were isolated in Escherichia coli by a general method in which nonluminous, transposon insertion mutants were used. Conditions necessary for light production in E. coli were examined. Stimulation of transcription of the genes for luciferase (lux A and lux B) was required for efficient synethesis of luciferase. To enhance transcription bacteriophage promoter elements were coupled to the cloned lux gene fragments.