DNA environment of the aerobactin iron uptake system genes in prototypic ColV plasmids

The Complete Nucleotide Sequence of pZM3, a 1970 FIA:FIB:FII Plasmid Carrying Antibiotic Resistance and Virulence Determinants

The multiresistance plasmid, pZM3, from a 1970 Salmonella enterica serovar Wien isolate from Algeria represents the multiresistance FIme-type plasmids conferring resistance to ampicillin, chloramphenicol, kanamycin, neomycin, sulfonamides, streptomycin, spectinomycin, tetracycline, and mercuric ions circulating in the Middle East in the 1970s. pZM3 was sequenced to determine the relationship between IS1936, the IS26-like insertion sequence it carries, and IS26. IS1936 is identical to IS26. pZM3 is a 166.8-kb plasmid with three replicons typed as FIA-1, FIB-1, and FII-1, consistent with other FIme plasmids. However, Tn3, containing the bla_TEM-1a ampicillin resistance gene, disrupts the FII repA gene. pZM3 also contains an IS1-flanked virulence region, including the sit and aerobactin operons, shared with many other FIB-1 virulence plasmids. The remaining resistance genes are located in a 44.7-kb complex resistance island that includes the Tn21-like transposon, Tn1935, identified previously. Relative to Tn21, Tn1935 includes an additional gene cassette, oxa1, and Tn4352 in tniA. Tn1935 is in the same Tn2670 context as Tn21 in NR1, and identity to NR1 extends beyond the IS1 flanking the catA1 gene. On the other side, IS1-mediated events have brought in a Tn10 remnant and inverted part of it, highlighting the role of IS1 in resistance region evolution. The backbone of pZM3 was found to be almost identical to that of pRSB225, recovered in Germany in 2013, and their resistance islands are in the same position. The pRSB225 resistance island has evolved in situ from the pZM3 configuration through an insertion, a replacement, and an inversion.

Plasmid-Encoded Iron Uptake Systems

Plasmids confer genetic information that benefits the bacterial cells containing them. In pathogenic bacteria, plasmids often harbor virulence determinants that enhance the pathogenicity of the bacterium. The ability to acquire iron in environments where it is limited, for instance the eukaryotic host, is a critical factor for bacterial growth. To acquire iron, bacteria have evolved specific iron uptake mechanisms. These systems are often chromosomally encoded, while those that are plasmid-encoded are rare. Two main plasmid types, ColV and pJM1, have been shown to harbor determinants that increase virulence by providing the cell with essential iron for growth. It is clear that these two plasmid groups evolved independently from each other since they do not share similarities either in the plasmid backbones or in the iron uptake systems they harbor. The siderophores aerobactin and salmochelin that are found on ColV plasmids fall in the hydroxamate and catechol group, respectively, whereas both functional groups are present in the anguibactin siderophore, the only iron uptake system found on pJM1-type plasmids. Besides siderophore-mediated iron uptake, ColV plasmids carry additional genes involved in iron metabolism. These systems include ABC transporters, hemolysins, and a hemoglobin protease. ColV- and pJM1-like plasmids have been shown to confer virulence to their bacterial host, and this trait can be completely ascribed to their encoded iron uptake systems.

Virulence factors of septicemic Escherichia coli strains

Extraintestinal pathogenic Escherichia coli strains (ExPEC) are the cause of a diverse spectrum of invasive human and animal infections, often leading to septicemia. This review deals with the virulence genes of septicemic ExPEC strains. We discuss the meaning of a virulence gene and survey the genomic, genetic and physiological studies on these strains. Apparently, there are a few virulence factors, which are conserved in the septicemic strains, implying that they are essential for the infection. For the other virulence-related genes a high level of diversity is observed, demonstrating that all stages of the infection can be mediated by a number of alternative virulence factors. The variable profile of virulence genes in septicemic E. coli strains, as well as a prevalence of mobility-related sequences point out the existence of a "mix and match" combinatorial system.

Nucleotide polymorphism in microcin V plasmids

DNA sequence polymorphism was determined for the microcin V gene cluster encoded on the microcin V plasmids of 12 natural isolates of Escherichia coli. These microcin V gene clusters are similar in DNA sequence, with only 10 of the 683 bp polymorphic. Further, the levels and patterns of microcin V gene cluster polymorphism differ from those of a chromosomal region, trpORF2, sequenced from each of the host isolates. These contrasting levels and patterns of polymorphism suggest that the microcin V gene cluster has experienced an evolutionary history different from that of the host.

Escherichia coli CoIV plasmid pRK100: genetic organization, stability and conjugal transfer

Uropathogenic Escherichia coli strains express chromosomal and plasmid-encoded virulence-associated factors such as specific adhesins, toxins and iron-uptake systems. A CoIV plasmid (pRK100) of a uropathogenic strain and its host KS533 were studied. The host strain encodes the K1 capsule, and P and S fimbriae, but neither haemolysin nor the cytotoxic-necrotic factor CNF1, indicating that this strain does not harbour a larger pathogenicity island. A restriction map of pRK100 was constructed on the basis of hybridization experiments and nucleotide sequencing. pRK100 harbours CoIV, the conserved replication region RepFIB, the aerobactin-uptake system, a RepFIC replicon and additionally Colla as well as transposon Tn5431. The location of the RepFIC replicon was similar to that in plasmid F. CoIV plasmids and F thus share a region spanning more than half the length of plasmid F. Even though their replication and transfer regions are homologous, CoIV plasmids are found only in E. coli strains. Among the four other species tested, conjugal transfer of pRK100 was demonstrated, with low frequency, only to Klebsiella pneumoniae, suggesting that a natural barrier effectively bars transfer. In vitro stability of the plasmid with integration into the chromosome to ensure maintenance in the presence of an incompatible plasmid was demonstrated.

Functional characterization of a replication initiator protein

Functional domains in the RepI replication initiator protein have been identified by classical and site-directed mutagenesis techniques. Mutations conferring an increase in plasmid copy number contained alterations in a key position of a putative helix-turn-helix DNA binding motif. The mutations did not appear to affect autorepressing functions. Regions of RepI important for autorepression were localized as well. Two classes of mutations resulting in diminished autorepression functions were identified. One class was distinguished by an elevated copy number, while the other class remained at the wild-type copy number level. Analysis of the various mutations leading to changes in copy number or autorepressing functions suggest that in some cases the autorepression and initiating functions of the RepI protein are separable. Finally, analysis with deletion clones suggests that the trans-acting autorepressing functions of RepI might depend on intermolecular coupling control.

Construction and biochemical characterization of recombinant cytoplasmic forms of the IucD protein (lysine:N6-hydroxylase) encoded by the pColV-K30 aerobactin gene cluster

The aerobactin gene cluster in pColV-K30 consists of five genes (iucABCD iutA); four of these (iucABCD) are involved in aerobactin biosynthesis, whereas the fifth one (iutA) encodes the ferriaerobactin outer membrane receptor. iucD encodes lysine:N6-hydroxylase, which catalyzes the first step in aerobactin biosynthesis. Regardless of the method used for cell rupture, we have consistently found that IucD remains membrane bound, and repeated efforts to achieve a purified and active soluble form of the enzyme have been unsuccessful. To circumvent this problem, we have constructed recombinant IucD proteins with modified amino termini by creating three in-frame gene fusions of IucD to the amino-terminal amino acids of the cytoplasmic enzyme beta-galactosidase. Two of these constructs resulted in the addition to the iucD coding region of a hydrophilic leader sequence of 13 and 30 amino acids. The other construct involved the deletion of the first 47 amino acids of the IucD amino terminus and the addition of 19 amino acids of the amino terminus of beta-galactosidase. Cells expressing any of the three recombinant IucD forms were found to produce soluble N6-hydroxylysine. One of these proteins, IucD439, was purified to homogeneity from the soluble fraction of the cell lysates, and it was capable of participating in the biosynthesis of aerobactin, as determined in vitro by a cell-free system and in vivo by a cross-feeding bioassay. A medium ionic strength of 0.25 (250 mM NaCl) or higher was required to maintain the protein in a catalytically functional, tetrameric state.(ABSTRACT TRUNCATED AT 250 WORDS)

Diphenylamine increases cloacin DF13 sensitivity in avian septicemic strains of Escherichia coli

Thirteen avian septicemic isolates of Escherichia coli were examined for the presence of the aerobactin iron transport system. All of the strains possessed a functional aerobactin system and hybridization experiments showed that the aerobactin genes were located on ColV-type plasmids in all cases. The expression of the aerobactin receptor IutA was also studied by determining the bacterial susceptibility to the bacteriocin cloacin DF13. Twelve of the 13 isolates were cloacin-resistant but became sensitive to this bacteriocin upon treatment with diphenylamine which caused a reduction in the amount of O-side chain lipopolysaccharide.

Colicin V virulence plasmids

ColV plasmids are a heterogeneous group of IncFI plasmids which encode virulence-related properties such as the aerobactin iron uptake system, increased serum survival, and resistance to phagocytosis. These plasmids have been found in invasive strains of Escherichia coli which infect vertebrate hosts including humans and livestock. Colicin V was the first colicin to be identified, in 1925, but not until the field experienced a renewed interest has the mechanism of colicin V activity been explored. As encoded by ColV plasmid pColV-K30, the aerobactin iron uptake system has been extensively investigated, but other ColV-encoded phenotypes remain largely uncharacterized. Restriction enzyme mapping of the 144-kb pColV-K30 and of the 80-kb pColV-B188 has facilitated systematic study, so that questions can be addressed by a molecular and comparative approach regarding the contributions of individual factors and plasmids to the virulence of host E. coli in model systems. The family of large ColV plasmids could be analogous to other families of large virulence plasmids, and insights gained from studying these plasmids should contribute to our understanding of cross-genetic interactions and the role of large plasmids in bacterial pathogenesis.

Virulence factors in Escherichia coli urinary tract infection

Uropathogenic strains of Escherichia coli are characterized by the expression of distinctive bacterial properties, products, or structures referred to as virulence factors because they help the organism overcome host defenses and colonize or invade the urinary tract. Virulence factors of recognized importance in the pathogenesis of urinary tract infection (UTI) include adhesins (P fimbriae, certain other mannose-resistant adhesins, and type 1 fimbriae), the aerobactin system, hemolysin, K capsule, and resistance to serum killing. This review summarizes the virtual explosion of information regarding the epidemiology, biochemistry, mechanisms of action, and genetic basis of these urovirulence factors that has occurred in the past decade and identifies areas in need of further study. Virulence factor expression is more common among certain genetically related groups of E. coli which constitute virulent clones within the larger E. coli population. In general, the more virulence factors a strain expresses, the more severe an infection it is able to cause. Certain virulence factors specifically favor the development of pyelonephritis, others favor cystitis, and others favor asymptomatic bacteriuria. The currently defined virulence factors clearly contribute to the virulence of wild-type strains but are usually insufficient in themselves to transform an avirulent organism into a pathogen, demonstrating that other as-yet-undefined virulence properties await discovery. Virulence factor testing is a useful epidemiological and research tool but as yet has no defined clinical role. Immunological and biochemical anti-virulence factor interventions are effective in animal models of UTI and hold promise for the prevention of UTI in humans.

Virulence-related genes in ColV plasmids of Escherichia coli isolated from human blood and intestines

DNA probes for the colicin V, traT, iss, and iu genes were used in this study of four representative ColV plasmids together with 200 Escherichia coli strains isolated from the stools of patients with diarrhea and 146 E. coli strains isolated from the blood of patients with bacteremia. The study indicated that the ColV plasmids are heterogeneous. Southern and colony hybridization analyses showed that in most of the colicin V-producing intestinal E. coli strains, the colicin V genes are located in the chromosome (14 of 16); in most of the colicin V-producing E. coli strains isolated from the blood, they are located in plasmids (18 of 22). In both intestinal and blood E. coli isolates, the traT, iss, and aerobactin receptor genes were present at similar frequencies, but the frequency of the aerobactin synthesis genes was significantly different. The aerobactin receptor gene was present in 25% of the intestinal E. coli strains that lack the aerobactin synthesis gene. In the blood isolates, the aerobactin synthesis and receptor genes were present at almost equal frequencies. Among the colicin V-producing isolates, the iss, traT, and iu genes were present in 95.5, 86.4, and 90.9% of the blood isolates and in only 68.8, 43.8, and 81.3% of the intestinal isolates, respectively. The ColV plasmids from blood isolates that were tested for the presence of traT, iss, and iu genes were homogeneous and had DNA sequences that hybridized with each of the probes. On the other hand, the two intestinal strains containing ColV genes in a plasmid were heterogeneous in regard to the carriage of these genes. The presence of ColV is not restricted to specific O types.

Genetics and molecular biology of siderophore-mediated iron transport in bacteria

The possession of specialized iron transport systems may be crucial for bacteria to override the iron limitation imposed by the host or the environment. One of the most commonly found strategies evolved by microorganisms is the production of siderophores, low-molecular-weight iron chelators that have very high constants of association for their complexes with iron. Thus, siderophores act as extracellular solubilizing agents for iron from minerals or organic compounds, such as transferrin and lactoferrin in the host vertebrate, under conditions of iron limitation. Transport of iron into the cell cytosol is mediated by specific membrane receptor and transport systems which recognize the iron-siderophore complexes. In this review I have analyzed in detail three siderophore-mediated iron uptake systems: the plasmid-encoded anguibactin system of Vibrio anguillarum, the aerobactin-mediated iron assimilation system present in the pColV-K30 plasmid and in the chromosomes of many enteric bacteria, and the chromosomally encoded enterobactin iron uptake system, found in Escherichia coli, Shigella spp., Salmonella spp., and other members of the family Enterobacteriaceae. The siderophore systems encoded by Pseudomonas aeruginosa, namely, pyochelin and pyoverdin, as well as the siderophore amonabactin, specified by Aeromonas hydrophila, are also discussed. The potential role of siderophore-mediated systems as virulence determinants in the specific host-bacteria interaction leading to disease is also analyzed with respect to the influence of these systems in the expression of other factors, such as toxins, in the bacterial virulence repertoire.

CoIV plasmids pCoIV-B188 and pCoIV-K30: genetic maps according to restriction enzyme sites and landmark phenotypic characteristics

The CoIV plasmids are large virulence plasmids of the incompatibility group IncFI. We have obtained the genetic maps of two of the most studied CoIV plasmids, pCoIV-B188 and pCoIV-K30, according to restriction enzyme sites and landmark phenotypic characteristics such as colicin V, the aerobactin iron uptake system, the transfer region, replication regions, and repeated sequences. Although the two plasmids differ in size (pCoIV-B188 is 80 kb and pCoIV-K30 is 144 kb), the maps reveal many regions which are apparently identical or very similar.

Distribution of the P-associated-pilus (pap) region among Escherichia coli from natural sources: evidence for horizontal gene transfer

Variation in chromosomal DNA in Escherichia coli was studied with probes specific for the P-associated-pilus (pap) region. The presence of DNA homologous to pap was determined by dot blots. Variation in the number of copies of pap and in the organization of internal and flanking sequences was determined by Southern blot hybridization. The 229 strains studied were also classified by O:K:H serotyping and multilocus enzyme electrophoresis. There was considerable heterogeneity in the presence of pap and distribution of pap-homologous DNA in these E. coli strains from natural sources. In general, there was less variation in pap among strains of the same specific O:K:H serotype and enzyme electrophoretic type than among random isolates. There were, however, E. coli strains identified as members of the same clone by O:K:H serotyping and enzyme electrophoresis that were pap positive and pap negative or had different Southern blot patterns for the pap probes (pap type). There were also isolates of the same pap type that differed in two of three O:K:H serotype antigens and the majority of enzymes that determined their enzyme electrophoretic type. These latter two observations were interpreted as evidence for the horizontal (infectious) transfer of the pap-homologous sequences among clones of E. coli.

Nucleotide sequence analysis and expression of the minimum REPI replication region and incompatibility determinants of pColV-K30

We sequenced the minimum REPI replication region and the incompatibility determinants of pColV-K30. The minimum replication region contains an open reading frame which corresponds to a 35-kilodalton (kDa) protein. Sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis with maxicells transformed with a number of deletion derivatives demonstrated that this replication region encodes a 39-kDa protein and also established the direction of transcription of the RepI protein gene. The 39-kDa polypeptide was identified as the trans-acting factor essential for replication of REPI-containing plasmids. A translated region of the nucleotide sequence of the RepI protein gene showed homology with the helix-turn-helix binding domains of a number of DNA-binding proteins and also with other plasmid replication proteins. Further nucleotide analysis of the REPI region revealed the presence of direct and inverted repeat sequences in the incE, incF, and ori regions. The REPI ori also contained a perfect DnaA-binding site in addition to a high frequency of occurrence of the DNA adenine methylation (dam) site 5'GATC3'.

Molecular cloning, expression, and regulation in Escherichia coli K-12 of a chromosome-mediated aerobactin iron transport system from a human invasive isolate of E. coli K1

We have cloned chromosomal genes determining the aerobactin iron transport system from the Escherichia coli K1 strain VW187. Mapping and hybridization experiments showed that the VW187 aerobactin region was identical to that of the plasmid ColV-K30. However, in the E. coli K-12 background, the biosynthesis of both siderophore and ferric aerobactin receptor encoded by the VW187-derived recombinant plasmids was not repressed by iron to the same extent found when a recombinant plasmid derived from pColV-K30 was used. RNA-DNA dot-blot hybridization experiments demonstrated that the aerobactin-specific mRNA synthesized by the VW187-derived clones was not iron regulated in E. coli K-12. In contrast, the synthesis of aerobactin and its receptor in strain VW187 was completely repressed by iron regardless of whether the recombinant plasmids originated from VW187 or pColV-K30. Similar results were obtained with gene fusions in which a promoterless lac operon was placed under the control of aerobactin promoter regions of either chromosome- or plasmid-mediated aerobactin systems. DNA sequencing of the chromosomal aerobactin promoter region showed changes in bases located immediately upstream to the -35 region compared with the corresponding region in pColV-K30, which is known to be part of the binding site for the Fur repressor protein.

New aerobactin-mediated iron uptake system in a septicemia-causing strain of Enterobacter cloacae

Unlike the great majority of the aerobactin-producing enteric bacteria documented in the literature, Enterobacter cloacae EK33, isolated from a case of human neonatal meningitis, did not show any homology at the DNA level with the prototype aerobactin system encoded by the ColV-K30 plasmid. However, both the nuclear magnetic resonance spectrum and fast-atom bombardment mass spectrometry of the siderophore purified from EK33 confirmed its identity with aerobactin. Bioassay screening of a gene library of total DNA of EK33 led to the isolation of several aerobactin-positive clones. Under conditions of iron limitation, these clones expressed in Escherichia coli a protein of 72 kilodaltons that reacted with antiserum raised against the pColV-K30 74-kilodalton aerobactin receptor, while the original E. cloacae strain synthesized an 85-kilodalton protein which also cross-reacted with the antiserum. Restriction endonuclease analysis of the cloned DNA confirmed the structural differences between the two aerobactin genetic systems.

Divergence of the aerobactin iron uptake systems encoded by plasmids pColV-K30 in Escherichia coli K-12 and pSMN1 in Aerobacter aerogenes 62-1

Although the aerobactin-mediated iron uptake system has been characterized genetically in Escherichia coli, the siderophore aerobactin was chemically characterized after purification from culture supernatants of Aerobacter aerogenes 62-1, a member of the Klebsielleae. We have cloned and mapped the genes encoding the aerobactin system genes of A. aerogenes 62-1 and begun characterization of the relevant proteins and enzymatic activities of this plasmid-mediated aerobactin system. Published chemical data indicate that the siderophore aerobactin of E. coli is the same molecule as the aerobactin of Aerobacter aerogenes 62-1, but we have found that both the genes and the complement of proteins making up the biosynthetic enzymes in the two systems have diverged. In contrast, the outer membrane receptors for ferric aerobactin of the two systems showed immunologic cross-reactivity, were of the same molecular size (74 kilodaltons), and were encoded by homologous DNA sequences.

Aerobactin production as a virulence factor: a reevaluation

Iron starvation is one of the major barriers that virulent bacteria must overcome in order to proliferate in the host. Virtually all microorganisms possess high affinity iron (III) transport systems mediated by low molecular weight iron specific chelators called siderophores, the synthesis of which is activated under iron-limiting conditions. Siderophore aerobactin is frequently produced by enterobacteria which cause various types of infections in humans and animals. The status of aerobactin production as a virulence factor is evaluated both from data derived from experimental infection systems and the actual presence of this siderophore in clinical isolates. Aerobactin appears to be an important contributor to extracellular pathogenesis (mostly, that of Escherichia coli strains causing septicaemia and urinary tract infections) and to the extracellular stages of growth of intracellular pathogens like Shigella. When invasive bacteria actually enter target cells, acquisition of iron seems to occur independently of siderophore production. The feasibility of an antimicrobial therapy aimed at interfering with siderophore functioning is discussed.

IS1-mediated mobility of the aerobactin system of pColV-K30 in Escherichia coli

Genes determining the high affinity iron transport system mediated by the siderophore aerobactin are flanked in the enterobacterial plasmid pColV-K30 by inverted repeats of IS1 sequences, suggesting that the aerobactin genes are part of a transposon. To study this possibility, the entire region between the two IS1 sequences was cloned as an 18 kb HindIII-BamHI restriction fragment in pUC8 giving plasmid pMO1. A number of derivatives of pMO1, in which aerobactin genes were tagged with a kanamycin resistance gene, were prepared in order to assess the ability of both IS1s to promote the formation of cointegrates with pCJ105, an F derivative devoid of insertion sequences. Mating-out assays indicated that both flanking IS1s were active in cointegrate formation at detectable frequencies. In some cases, the cointegrates could be resolved, the final result being a transposition-like event for the entire aerobactin system.

Iron and virulence in the family Enterobacteriaceae

The ability of bacterial pathogens to acquire iron in the host is an essential component of the disease process. Pathogenic Enterobacteriaceae spp. may either scavenge host iron sources such as heme or induce high-affinity iron-transport systems to remove iron from host proteins. The ease with which iron is acquired from the host will be at least partially determined by the iron status of the host at the time of infection. In response to infection, mammalian hosts reduce serum iron levels and withhold iron from the invading microorganisms. Thus the competition for iron is an active process which influences the outcome of a host-bacterial interaction.

Novel incompatibility and partition loci for the REPI replication region of plasmid ColV-K30

The minimum pColV-K30 REPI region necessary for replication was located within a ca. 1.3-kilobase DNA segment. Adjacent to the essential replication sequences, there are two DNA regions that express incompatibility with plasmids containing the F secondary replicon of the F EcoRI fragment f7. One of these regions corresponds to incE, already described in that F plasmid fragment which expresses incompatibility with f7-containing plasmids. The other is a novel sequence that we designated incF, which confers incompatibility with REPI, P307, and f7 derivatives, cis-acting pColV-K30 sequences conferring stability to REPI-containing plasmids were also identified and localized noncontiguous to REPI, ca. 20 kilobases downstream from the aerobactin iron transport genes, which were thus flanked by REPI and its partition (par) sequences.