Mechanisms by which transcription can regulate somatic hypermutation.

Mechanisms for somatic hypermutation (SHM) have proven elusive. An actively transcribed substrate was analyzed to elucidate the role of stem-loop structures (SLSs) in SHM. Analysis with a new computer algorithm indicates that the location and mutability of a base are regulated by: (a) the extent to which it is unpaired, (b) the degree to which it is exposed by stabilization of SLSs containing and flanking it, and (c) the level of transcription that drives supercoiling, which creates and stabilizes SLSs containing unpaired bases vulnerable to mutation. New mechanisms are described by which transcription can differentially stabilize SLSs harboring targeted bases and establish specific base exposure patterns. Assuming that transcription levels correlate with the magnitude of superhelicity induced and the lengths of ssDNA forming SLSs, this analysis accounts for the location of all mutable bases during SHM.

Establishing a direct role for the Bartonella bacilliformis invasion-associated locus B (IalB) protein in human erythrocyte parasitism.

The invasion-associated locus A and B genes (ialAB) of Bartonella bacilliformis were previously shown to confer an erythrocyte-invasive phenotype upon Escherichia coli, indirectly implicating their role in virulence. We report the first direct demonstration of a role for ialB as a virulence factor in B. bacilliformis. The presence of a secretory signal sequence and amino acid sequence similarity to two known outer membrane proteins involved in virulence suggested that IalB was an outer membrane protein. To develop an antiserum for protein localization, the ialB gene was cloned in frame into an expression vector with a six-histidine tag and under control of the lacZ promoter. The IalB fusion protein was purified by nickel affinity chromatography and used to raise polyclonal antibodies. IalB was initially localized to the bacterial membrane fraction. To further localize IalB, B. bacilliformis inner and outer membranes were fractionated by sucrose density gradient centrifugation and identified by appearance, buoyant density (rho), and cytochrome b content. Inner and outer membrane proteins were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and IalB was positively identified by Western blot. Contrary to expectations, IalB was localized to the inner membrane of the pathogen. To directly demonstrate a role for IalB in erythrocyte parasitism, the B. bacilliformis ialB gene was disrupted by insertional mutagenesis. The resulting ialB mutant strain was complemented in trans with a replicative plasmid encoding the full-length ialB gene. PCR and high-stringency DNA hybridization confirmed mutagenesis and transcomplementation events. Abrogation and restoration of ialB expression was verified by SDS-PAGE and immunoblotting. In vitro virulence assays showed that mutagenesis of ialB decreased bacterial association and invasion of human erythrocytes by 47 to 53% relative to controls. Transcomplementation of ialB restored erythrocyte association and invasion rates to levels observed in the parental strain. These data provide direct evidence for IalB's role in erythrocyte parasitism and represent the first demonstration of molecular Koch's postulates for a Bartonella species.

Experimental model of human body louse infection using green fluorescent protein-expressing Bartonella quintana.

A laboratory colony of human body lice was experimentally infected by feeding on rabbits made artificially bacteremic with a green fluorescent protein-expressing Bartonella quintana. B. quintana was detected in the gut and feces until death but not in the eggs. The life span of the lice was not modified. The rabbit model should provide valuable clues to the role of lice in the transmission of B. quintana.

Hemin-binding surface protein from Bartonella quintana.

Bartonella quintana, the agent of trench fever and a cause of endocarditis and bacillary angiomatosis in humans, has the highest reported in vitro hemin requirement for any bacterium. We determined that eight membrane-associated proteins from B. quintana bind hemin and that a approximately 25-kDa protein (HbpA) was the dominant hemin-binding protein. Like many outer membrane proteins, HbpA partitions to the detergent phase of a Triton X-114 extract of the cell and is heat modifiable, displaying an apparent molecular mass shift from approximately 25 to 30 kDa when solubilized at 100 degrees C. Immunoblots of purified outer and inner membranes and immunoelectron microscopy with whole cells show that HbpA is strictly located in the outer membrane and surface exposed, respectively. The N-terminal sequence of mature HbpA was determined and used to clone the HbpA-encoding gene (hbpA) from a lambda genomic library. The hbpA gene is 816 bp in length, encoding a predicted immature protein of approximately 29.3 kDa and a mature protein of 27.1 kDa. A Fur box homolog with 53% identity to the Escherichia coli Fur consensus is located upstream of hbpA and may be involved in regulating expression. BLAST searches indicate that the closest homologs to HbpA include the Bartonella henselae phage-associated membrane protein, Pap31 (58.4% identity), and the OMP31 porin from Brucella melitensis (31.7% identity). High-stringency Southern blots indicate that all five pathogenic Bartonella spp. possess hbpA homologs. Recombinant HbpA can bind hemin in vitro; however, it does not confer a hemin-binding phenotype upon E. coli. Intact B. quintana treated with purified anti-HbpA Fab fragments show a significant (P < 0.004) dose-dependent decrease in hemin binding relative to controls, suggesting that HbpA plays an active role in hemin acquisition and therefore pathogenesis. HbpA is the first potential virulence determinant characterized from B. quintana.

Development of a system for genetic manipulation of Bartonella bacilliformis.

Lack of a system for site-specific genetic manipulation has severely hindered studies on the molecular biology of all Bartonella species. We report the first site-specific mutagenesis and complementation for a Bartonella species. A highly transformable strain of B. bacilliformis, termed JB584, was isolated and found to exhibit a significant increase in transformation efficiency with the broad-host-range plasmid pBBR1MCS-2, relative to wild-type strains. Restriction analyses of genomic preparations with the methylation-sensitive restriction enzymes ClaI and StuI suggest that strain JB584 possesses a dcm methylase mutation that contributes to its enhanced transformability. A suicide plasmid, pUB1, which contains a polylinker, a pMB1 replicon, and a nptI kanamycin resistance cassette, was constructed. An internal 508-bp fragment of the B. bacilliformis flagellin gene (fla) was cloned into pUB1 to generate pUB508, a fla-targeting suicide vector. Introduction of pUB508 into JB584 by electroporation generated eight Kan(r) clones of B. bacilliformis. Characterization of one of these strains, termed JB585, indicated that allelic exchange between pUB508 and fla had occurred. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, immunoblotting, and electron microscopy showed that synthesis of flagellin encoded by fla and secretion/assembly of flagella were abolished. Complementation of fla in trans was accomplished with a pBBR1MCS recombinant containing the entire wild-type fla gene (pBBRFLAG). These data conclusively show that inactivation of fla results in a bald, nonmotile phenotype and that pMB1 and REP replicons make suitable B. bacilliformis suicide and shuttle vectors, respectively. When used in conjunction with the highly transformable strain JB584, this system for site-specific genetic manipulation and complementation provides a new venue for studying the molecular biology of B. bacilliformis.

The IalA invasion gene of Bartonella bacilliformis encodes a (de)nucleoside polyphosphate hydrolase of the MutT motif family and has homologs in other invasive bacteria.

The product of the ialA invasion gene of Bartonella bacilliformis has been expressed as a thioredoxin fusion protein. It is a (di)nucleoside polyphosphate hydrolase of the MutT motif protein family with strong sequence similarity to plant diadenosine tetraphosphate hydrolases. It hydrolyses nucleoside and dinucleoside polyphosphates with four or more phosphate groups, always producing an NTP as one product. Diadenosine tetraphosphate (Ap4A) is the preferred substrate with a Km of 10 microM and a kcat of 3.0 s-1. It is inhibited by Ca2+ and F- (Ki = 30 microM). Hydrolysis of Ap4A in H218O yielded [18O]AMP as the only labelled product. In terms of sequence, reaction mechanism and properties, IalA is very similar to eukaryotic Ap4A hydrolases and unlike previously described bacterial Ap4A hydrolases. Homologs are present in the genomes of other invasive pathogens. They may function to reduce stress-induced dinucleotide levels during invasion and so enhance pathogen survival.

Mutations in Bartonella bacilliformis gyrB confer resistance to coumermycin A1.

This study describes the first isolation and characterization of spontaneous mutants conferring natural resistance to an antibiotic for any Bartonella species. The Bartonella bacilliformis gyrB gene, which encodes the B subunit of DNA gyrase, was cloned and sequenced. The gyrB open reading frame (ORF) is 2,079 bp and encodes a deduced amino acid sequence of 692 residues, corresponding to a predicted protein of approximately 77.5 kDa. Sequence alignment indicates that B. bacilliformis GyrB is most similar to the GyrB protein from Bacillus subtilis (40.1% amino acid sequence identity) and that it contains the longest N-terminal tail (52 residues) of any GyrB characterized to date. The cloned B. bacilliformis gyrB was expressed in an Escherichia coli S30 cell extract and was able to functionally complement a temperature-sensitive E. coli Cour gyrB mutant (strain N4177). We isolated and characterized spontaneous mutants of B. bacilliformis resistant to coumermycin A1, an antibiotic that targets GyrB. Sequence analysis of gyrB from 12 Cour mutants of B. bacilliformis identified single nucleotide transitions at three separate loci in the ORF. The predicted amino acid substitutions resulting from these transitions are Gly to Ser at position 124 (Gly124-->Ser), Arg184-->Gln, and Thr214-->Ala or Thr214-->Ile, which are analogous to mutated residues found in previously characterized resistant gyrB genes from Borrelia burgdorferi, E. coli, Staphylococcus aureus, and Haloferax sp. The Cour mutants are three to five times more resistant to coumermycin A1 than the wild-type parental strain.

Cloning, functional expression, and complementation analysis of an inorganic pyrophosphatase from Bartonella bacilliformis.

We have cloned the inorganic pyrophosphatase gene (ppa) from the facultative intracellular pathogen Bartonella bacilliformis and characterized its encoded product. The 531-bp gene is located approximately 1 kb downstream of, and in opposite orientation to, the invasion-associated locus (ialAB) of B. bacilliformis. The predicted protein encoded by ppa is 177 amino acid residues, which is in agreement with in vitro and in vivo synthesis of a protein with an apparent molecular mass of 22-23 kDa. The predicted B. bacilliformis pyrophosphatase (PPase) sequence is 53% identical and 85% similar to the E. coli PPase (EC 3.6.1.1), and contains all 12 of the amino acid residues implicated in the catalytic active site. The isolated B. bacilliformis PPase exhibits an activity of 51 +/- 2 mumol PO4 released/(mg protein.min) at 28 degrees C and pH 8, and is sensitive to inhibition by Ca2+. In keeping with other prokaryotic PPases, B. bacilliformis PPase activity occurs from pH 6 to 10 (optimal pH = 8) and demonstrates high thermostability in the presence of Mg2+ (highest activity at 55 degrees C, relative activity = 80 +/- 3% at pH 8). The cloned B. bacilliformis ppa is able to genetically complement a ppa- mutant strain of E. coli.

Cell entry and the pathogenesis of Bartonella infections.

Erythrocyte parasitism, or hemotrophy, is not a common strategy for bacteria. However, Bartonella species are elegantly adapted to parasitize a variety of cell types including red blood cells. Bartonella bacilliformis, a useful model organism for the genus, has been used to study virulence determinants involved in colonization, attachment and invasion of host cells.

Nucleotide sequence analysis of the 23S ribosomal RNA-encoding gene of Bartonella bacilliformis.

We report the cloning and characterization of the 23S ribosomal RNA (rRNA)-encoding gene (rDNA) of Bartonella bacilliformis (Bb). The 2821-bp gene is preceded by an 11-nucleotide (nt) inverted repeat (IR) located 81 nt upstream in the tRNA(Ala)-23S rDNA intergenic spacer. The gene is followed by an 8-nt IR, five nt downstream in the 23S-5S rDNA intergenic spacer. The nt sequence of the Bb 23S rDNA is most similar to the 23S rDNA of Rhodopseudomonas palustris (Rp), with 85.4% sequence identity. The Bb 23S rDNA has 77.8% identity to the same gene from Escherichia coli (Ec). Secondary structure predictions indicate that the large subunit (LSU) Bb rRNA contains two smaller stem-loops at nt 1459-1544 and 1658-1685, as compared to the corresponding loops from Ec (nt 1405-1597 and 1707-1751, respectively). In addition, the Bb 23S rRNA has a large 72-nt stem-loop at nt 130-201, as compared to the Ec 18-nt stem-loop (nt 131-148). There is no Bb homologue of the 15-nt stem-loop at the 3' end of the Ec molecule (nt 2791-2805). The Bb 23S rRNA lacks the large stem-loop present in the LSU rRNA of closely related Rhodobacter sphaeroides (Rs) (nt position 1225-1331) which is thought to be involved in cleavage of 23S RNA precursor molecules into 16S and 14S rRNA species. This is the first LSU rDNA nt sequence for any member of the Bartonellaceae family.

Characterization of a two-gene locus from Bartonella bacilliformis associated with the ability to invade human erythrocytes.

Bartonella bacilliformis, the agent of human Oroya fever, invades erythrocytes and causes a severe hemolytic anemia. The ability of two minimally invasive strains of Escherichia coli (DH5 alpha and HB101) to invade human erythrocytes was enhanced 6- to 39-fold by transformation with pIAL1, a plasmid containing a 1,469-bp BamHI fragment from the B. bacilliformis chromosome. Invasiveness was confirmed by gentamicin protection and transmission electron microscopy. DNA hybridization analysis confirmed the presence of the locus in B. bacilliformis KC583 and KC584 and its absence in E. coli chromosomal DNA. Sequencing of the DNA insert of pIAL1 revealed tandem open reading frames of 510 and 558 bp, designated ialA and ialB, respectively. Invasion assays with E. coli containing only an ialA or ialB recombinant suggest that both genes are necessary for invasiveness. The ialA gene is predicted to code for a polypeptide of 170 amino acids (20.1 kDa), and ialB is predicted to code for a polypeptide of 186 amino acids (19.9 kDa). In vitro transcription and translation of pIAL1 produced insert-specific protein bands with masses of approximately 21 and 20 kDa when analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Expression of ialA and ialB in E. coli maxicells produced proteins with masses of approximately 21 kDa (IalA) and 18 kDa (IalB). Maxicell and computer analyses suggest that IalB contains an N-terminal secretory signal sequence which is posttranslationally cleaved. Searches of various DNA and protein databases revealed that IalA contains an N-terminal region of 35 amino acids with a high degree of homology to an NTPase consensus domain. There is 63.6% sequence conservation between the IalB protein and the invasion-associated protein Ail of Yersinia enterocolitica.

Transformation of Bartonella bacilliformis by electroporation.

Bartonella bacilliformis is a member of the order Rickettsiales, family Bartonellaceae. The bacterium is an intracellular parasite of human erythrocytes. To date, members of the family Bartonellaceae have not been transformed by standard chemical methods. We report the first successful transformation of a member of the Bartonellaceae family, B. bacilliformis, by the method of electroporation. The optimal conditions for electroporation of B. bacilliformis include a field strength of 12.5 kV/cm and a time constant of 5 ms using 0.2-cm cuvettes. With these parameters and the cosmid pEST (RK2 replicon), a transformation efficiency of 7.8 x 10(5) was obtained. Transformants were readily cultured on medium containing kanamycin sulfate at concentrations ranging from 15 to 600 micrograms/mL. Bacterial survival was approximately 31% under optimal electroporation conditions, and the maximal number of transformants was obtained with 80 ng of pEST DNA. Bartonella bacilliformis was verified as the transformed organism by a comparison of transformant protein profiles with those of wild-type B. bacilliformis using sodium dodecyl sulfate polyacrylamide gel electrophoresis, and detection of the exogenous plasmid in DNA from the transformed bacteria by DNA hybridization. Transformations using the plasmids pMK20, pML31, and pUCK18 (containing the replicons ColE1, F, and pMB1, respectively) were not successful.

Identification of outer membrane proteins of Bartonella bacilliformis.

Purification of the outer membrane of Bartonella bacilliformis by sucrose step gradient centrifugation and analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) suggest that 14 proteins, ranging from 11.2 to 75.3 kDa, are located in the outer membrane of the pathogen. On the basis of M(r)s, eleven of these proteins have counterparts which are labeled by extrinsic radioiodination of intact bartonellae, and two of the proteins are visibly sensitive to extrinsic proteinase K digestion in analysis by SDS-PAGE. While nearly all the extrinsically radioiodinated proteins could be immunoprecipitated with rabbit antibartonella hyperimmune serum, proteins of 31.5, 42, and 45 kDa were prominent immunoprecipitants. Purified lipopolysaccharide from the outer membrane of B. bacilliformis produced a diffuse band of approximately 5 kDa on SDS-PAGE and was not detectable on immunoblots developed with rabbit antibartonella hyperimmune antiserum.

Characterization of the 16S-23S rRNA intergenic spacer of Bartonella bacilliformis.

The 16S-23S intergenic spacer region from the ribosomal RNA (rRNA) operon of Bartonella bacilliformis was cloned and characterized. The spacer is 906 nucleotides (nt) in length and contains the genes encoding isoleucine-tRNA (tRNA(Ile)) and alanine-tRNA (tRNA(Ala)). The tRNA-encoding genes are separated by 122 nt and are centrally located in the 16S-23S spacer region, with approx. 300 flanking nt. Genes encoding tRNA(Ile) and tRNA(Ala) have 88.3 and 93.4% sequence identity, respectively, to the homologous genes of Rhodobacter sphaeroides.

Characterization of Bartonella bacilliformis flagella and effect of antiflagellin antibodies on invasion of human erythrocytes.

Bartonella bacilliformis is the etiologic agent of Oroya fever in humans. Flagellum-mediated motility has been postulated as a major virulence factor for invasion of host cells. To address this hypothesis, we purified and characterized flagella from strain KC584 and then assessed their role in human erythrocyte association and invasion. Electron microscopy of the flagellar preparation showed a high concentration of filaments with a mean wavelength of 800 nm. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis, immunoblot analysis, and KBr density gradient centrifugation indicated that the flagellar filament is composed of a polypeptide of 42 kDa. The flagellin is partially (ca. 50%) resistant to treatment with trypsin. The first 17 amino acid residues of the N terminus of the mature flagellin protein are GAAILTNDNAMDALQDL and show approximately 46% sequence identity to the residues of the N termini of two Caulobacter crescentus flagellin proteins. A monospecific polyclonal antibodies to the flagellin protein was generated, and its specificity was verified by both immunoblot and immunogold analyses. Human erythrocyte invasion assays performed with bartonellae exposed to the antiflagellin antiserum showed a significant decrease in bacterial association with and invasion of human erythrocytes in comparison with that in bartonellae exposed to preimmune rabbit serum or phosphate-buffered saline (PBS) controls. These results suggest that flagella are an important component in the invasiveness of B. bacilliformis.

Characterization of the fMet initiator tRNA gene of Bartonella bacilliformis.

A ribosomal RNA operon was cloned from the agent of human Oroya fever, Bartonella bacilliformis. The 3' end of the operon contains a 77-nucleotide (nt) N-formylmethionine (fMet) initiator tRNA-encoding gene with 100% sequence identity to the fMet tRNA-encoding gene of Rhodobacter sphaeroides. The 3' region downstream from the gene has an 8-nt inverted repeat and 28 contiguous direct repeats of the heptamer 5'-TTCTCTA. To date, B. bacilliformis and R. sphaeroides are the only known eubacteria which have an fMet tRNA-encoding gene within the 3' end of their rRNA operons.

Cloning and sequence analysis of a hemolysin-encoding gene from Pseudomonas paucimobilis.

We report the cloning, expression and nucleotide (nt) sequence of a beta-hemolysin-encoding gene, termed hlyA, from Pseudomonas paucimobilis. A genomic DNA library of the pseudomonad was constructed in Escherichia coli using the plasmid vector, pUC19. The hlyA gene was cloned by screening for a beta-hemolytic phenotype in E. coli transformants and was mapped to a 1100-bp PstI-SmaI fragment. The nt sequence analysis of the 1100-bp insert revealed a 789-bp open reading frame which is preceded by a 10-nt purine-rich sequence with a possible ribosome-binding site of GGA. The ORF terminates with a single UGA stop codon and is immediately followed by a large inverted repeat with 27-bp arms which may serve as a Rho-factor-independent transcriptional terminator. The hlyA gene codes for a protein of 263 amino acids (aa) residues with a deduced relative molecular mass (M(r)) of 29,695 and a predicted pI value of 11.5. Expression of hlyA from recombinant DNA in E. coli occurred regardless of insert orientation in the vector and produced a 29-kDa protein. Confirmation of P. paucimobilis as the source of the cloned hlyA gene was determined by DNA hybridization. A search of various nt and aa sequence databases revealed no homologues to hlyA or its encoded protein.