Novel Tn4371-ICE like element in Ralstonia pickettii and genome mining for comparative elements

Background

Integrative Conjugative Elements (ICEs) are important factors in the plasticity of microbial genomes. An element related to the ICE Tn4371 was discovered during a bioinformatic search of the Ralstonia pickettii 12J genome. This element was analysed and further searches carried out for additional elements.

A PCR method was designed to detect and characterise new elements of this type based on this scaffold and a culture collection of fifty-eight Ralstonia pickettii and Ralstonia insidiosa strains were analysed for the presence of the element.

Results

Comparative sequence analysis of bacterial genomes has revealed the presence of a number of uncharacterised Tn4371-like ICEs in the genomes of several β and γ- Proteobacteria. These elements vary in size, GC content, putative function and have a mosaic-like structure of plasmid- and phage-like sequences which is typical of Tn4371-like ICEs. These elements were found after a through search of the GenBank database. The elements, which are found in Ralstonia, Delftia, Acidovorax, Bordetella, Comamonas, Acidovorax, Congregibacter, Shewanella, Pseudomonas Stenotrophomonas, Thioalkalivibrio sp. HL-EbGR7, Polaromonas, Burkholderia and Diaphorobacter sp. share a common scaffold. A PCR method was designed (based on the Tn4371- like element detected in the Ralstonia pickettii 12J genome) to detect and characterise new elements of this type.

Conclusion

All elements found in this study possess a common scaffold of core genes but contain different accessory genes. A new uniform nomenclature is suggested for ICEs of the Tn4371 family. Two novel Tn4371-like ICE were discovered and characterised, using the novel PCR method described in two different isolates of Ralstonia pickettii from laboratory purified water.

Introducing principles of validation into biochemistry and biotechnology courses: Practical concepts and a framework for active learning

Although undergraduate biochemistry and biotechnology courses teach the concept of accuracy and precision during practical laboratory sessions, the formal teaching of validation methodologies receives little attention. An increasing number of biochemistry and biotechnology graduates are finding work in industry in the area of industrial validation associated with biopharmaceutical, diagnostics, biomedical device, and pharmaceutical validation. We have introduced a structured introduction to validation into our undergraduate industrial biochemistry programme to illustrate the importance of validation within a framework of good manufacturing practice (GMP) and to show how validation is essential for regulatory compliance.

Ralstonia pickettiiin environmental biotechnology: potential and applications

Xenobiotic pollutants such as toluene and trichloroethylene are released into the environment by various industrial processes. Ralstonia pickettii possess significant biotechnological potential in the field of bioremediation and has demonstrated the ability to breakdown many of these toxic substances. Here, we provide a description of the major compounds that various strains of R. pickettii are capable of degrading and a brief review of their breakdown pathways and an argument for its use in bioremediation.

Theorf4 gene of the enterobacterial ICE, R391, encodes a novel UV-inducible recombination directionality factor, Jef, involved in excision and transfer of the ICE

The enterobacterial mobile genetic element R391, the prototype ICE (integrating-conjugative element) of the SXT/R391 family, shows increased conjugative transfer following UV irradiation. This is dependent on a functioning R391 orf4 gene, which is adjacent to the element encoded integrase gene, int. orf4 mutants fail to form a detectable circular transfer intermediate, do not show UV induced transfer and show a much reduced general transfer ability. The orf4 gene product, termed Jef (IncJ excision factor), shows little homology to anything currently in the nucleotide or protein databases. It is predicted to encode a 66 amino acid, 8.03 kDa, basic, DNA-binding protein with an iso-electric point of pH 8.1: these characteristics being similar to those of recombinational directionality factors involved in excision. Jef expression is up-regulated upon UV irradiation as demonstrated by real-time reverse transcriptase PCR and is controlled by two element encoded genes orf90 and orf91, which show similarity to the transcriptional activator complex FlhC and FlhD. orf4, orf90 and orf91 are conserved in all the SXT/R391-like elements sequenced to date including SXT, ICESpuPO1 and ICEVchMex1. orf4 is also conserved in other SXT/R391 family members such as R997, R392, R705 and pMERPH as shown by sequencing amplicons from these ICEs generated using orf4 specific primers.

A novel ICE in the genome of Shewanella putrefaciens W3-18-1: comparison with the SXT/R391 ICE-like elements

A novel R391-like ICE (integrating conjugative element) has been detected in the 4.2 MB genome of Shewanella putrefaciens W3-18-1 located on three different contigs. Assembly of the ICE encoding contigs based on similarity with R391 revealed a mosaic element of plasmid, phage and transposon-like sequences typical of SXT/R391 ICE-like elements. The element, which is 110 057 bp in length, was highly similar to R391 sequences, with most related ORFs showing >96% amino acid sequence identity. The element, designated ICESpuPO1, contained a number of inserts determining resistance to copper and other heavy metals and a broad-spectrum RND efflux pump similar to antibiotic efflux systems. The element was integrated into the Shewanella prfC gene in a manner similar to related ICE-like elements. The chromosomal element junctions contained a 17-bp SXT/R391-like attL and attR site and an unannotated ORF between attL and the ICE integrase encoding a putative recombinational directional factor necessary for excision, with 100% amino acid identity to the R391 ORF4 product.

Ralstonia pickettii: a persistent gram-negative nosocomial infectious organism

Non-fermenting Gram-negative bacilli create a significant problem in clinical settings, being a widespread cause of nosocomial infections. They are opportunistic pathogens that take advantage of underlying conditions and diseases. Ralstonia pickettii, a non-fermenting Gram-negative bacillus, is regarded as being of minor clinical significance; however, many instances of infections with this organism are reported in the literature. Infections can include bacteraemia/septicaemia caused by contaminated solutions, e.g. distilled water, water for injection and aqueous chlorhexidine solutions. Cases of pseudobacteraemia have been recorded in association with R. pickettii, as have many cases of unusual infections, some of which were very invasive and severe, e.g. meningitis, septic arthritis and osteomyelitis. Six cases of death in four separate instances have also been recorded related to R. pickettii. This review illustrates that R. pickettii is a more important pathogen than was thought previously.

Molecular tools to detect the IncJ elements: a family of integrating, antibiotic resistant mobile genetic elements

The IncJ group of enterobacterial mobile genetic elements, which include R391, R392, R705, R997 and pMERPH, have been shown to be site-specific integrating elements encoding variable antibiotic and heavy metal resistance genes. They insert into a specific 17-bp site located in the prfC gene, encoding peptide release factor 3, in Escherichia coli and other hosts. A key feature of known IncJ elements is the presence of a site-specific recombination module consisting of an attachment site on the element and an integrase-encoding gene of the tyrosine recombinase class, which promotes integration between the attachment site on the element and a similar site on the host chromosome. We have cloned and sequenced the integrases from a number of known IncJ elements and designed PCR primers for specific amplification of this gene. Using conserved regions of enterobacterial prfC genes upstream and downstream of the insertion site, and conserved sequences at the ends of the integrated IncJ elements, we have designed specific primers to amplify across the integrated IncJ attL and attR junction fragments. Alignment of over 30 enterobacterial prfC-like genes indicates that the primers designed to amplify attR junction would amplify IncJ element: host junctions from a wide variety of hosts. The IncJ elements have been shown to sensitise recA(+)E. coli K12 strains to UV irradiation. A simple and rapid procedure for demonstrating this effect is described. These tools should enable the rapid detection of such elements in clinical and environmental settings.

Pulsed field gel electrophoresis to rapidly detect the presence of IncJ conjugative transposon-like elements

AIMS

To develop a screening method to detect the presence of the IncJ group of integrating conjugative transposon-like elements upon transfer to Escherichia coli.

METHODS AND RESULTS

The unique insertion site of known IncJ elements, the prfC gene, is located in a region of the E. coli chromosome between 98.5 and 100 min on the E. coli genetic map. Using pulsed field gel electrophoresis and the rare cutting restriction enzymes SfiI and XbaI insertions of IncJ elements and an estimate of their size could be determined physically.

CONCLUSIONS

This method allows initial screening of putative IncJ conjugative transposon-like elements by physical determination of their integration.

SIGNIFICANCE AND IMPACT OF THE STUDY

IncJ-like elements, which appear to be highly homologous to the prototype IncJ element R391, have been found associated with recent epidemic outbreaks of cholera in a number of locations worldwide. Because of their integrative biology this method provides the first initial screening method to physically determine their presence upon transfer to E. coli.

Detailed analysis of the insertion site of the mobile elements R997, pMERPH, R392, R705 and R391 in E. coli K12

The IncJ group of mobile elements have not been extensively studied until recently, due to the inability to isolate extrachromosomal DNA from IncJ-strains. Sequence analysis of the prototype IncJ element, R391, revealed it to be a mosaic structure, integrated into the prfC gene in E. coli. Using inverse PCR (iPCR), we localised the other available IncJ elements (R392, R705, R997 and pMERPH) site of insertion to a 17-bp sequence, within the 5' end of prfC at 99.31 min on the E. coli chromosome, and confirmed this for R391. Despite disrupting prfC, the IncJ's encode novel promoter and 5' sequences, restoring function of the disrupted prfC. Sequence analysis of the elements ends revealed that they contain integrase genes, which share extensive homologies among the group, despite being isolated from broad geographic locations. The elements excise from the host chromosome by recombination between their attL and attR sites, with subsequent recombination between the attP sites on the circular forms and the attB sites in the host genomes. The attB site is highly conserved and found in many different bacteria, suggesting a possible broad host range.

Pre-exposure to UV irradiation increases the transfer frequency of the IncJ conjugative transposon-like elements R391, R392, R705, R706, R997 and pMERPH and isrecA+dependent

The enteric conjugative transposon-like IncJ elements R391, R392, R705, R706 and pMERPH, all demonstrated increased conjugative transfer upon UV irradiation. The transfer frequency increased on average from its basal rate of 10(-5) to 10(-3) per recipient, upon pre-exposure to UV irradiation. However, the transfer frequency of R997, which was higher than the other IncJ elements at 10(-3) per donor, showed a smaller increase. This effect was shown to be recA+ dependent in all cases. Using PCR primers directed outwards from the ends of the integrated R391 element it was observed that a circular intermediate of the element forms within the host, which has been proposed to be a transfer intermediate. Using real-time PCR, it was determined that the amount of the circular intermediate produced increased substantially upon UV irradiation.

The effect of choice of sterilisation method on the biocompatibility and biodegradability of SIS (small intestinal submucosa)

SIS (small intestinal submucosa) is a 3D extracellular matrix (ECM) material of porcine origin. It has a complex composition predominantly composed of collagen type I. SIS is rapidly absorbed, supports early and abundant new vessel growth, and serves as a template for the reconstructive remodelling of several body tissues. Currently SIS products are sterilised using ethylene oxide, gamma irradiation and e-beam irradiation. It is not known how they affect the materials properties such as structure, mechanical strength and biocompatibility. This study investigated the influence of each sterilisation method on the biocompatibility and biodegradation of SIS using L929 mouse fibroblasts. SIS samples were sterilised by each of the above methods under standard conditions. The samples were subjected to hydrolytic degradation conditions for specific periods of time. All sterilisation methods resulted in an increase in the rate of sample degradation. The study indicated that over time e-beam irradiation caused the greatest % weight loss. Applying sample extracts to L929 mouse fibroblasts assessed the biocompatibility of the degradation products. The % cellular protein and % metabolic activity were then assessed using the BCA assay and MTT assay, respectively. All SIS samples caused an increase in both cellular protein production and metabolic activity. Initially samples sterilised by ETO had the greatest effect but this decreased after 28 days. Unsterile samples were found to have a slower more prolonged influence. It is thought that the components released may include extractable growth factors and further studies are required to confirm this.

The role of conjugative transposons in the Enterobacteriaceae

Although widely studied in gram-positive Streptococci and in the gram-negative Bacteroides, there is a scarcity of information on the occurrence and nature of conjugative transposon-like elements in the well-studied Enterobacteriaceae. In fact, some of the major reviews on conjugative transposons prior to 1996 failed to mention their occurrence in this group. Recently, their presence has been reported in Salmonella, Vibrio and Proteus species, and in some cases such as the SXT element in Vibrio and the IncJ group element CTnR391, there has been some molecular characterization. The elements thus far examined appear to be larger than the common gram-positive conjugative transposons and to be mosaic in structure, with genes derived from several sources. Recent evidence suggests that in the Enterobacteriaceae the elements may be related to enteric pathogenicity islands. The evolution, distribution and role of these elements in the Enterobacteriaceae is discussed.

R391: a conjugative integrating mosaic comprised of phage, plasmid, and transposon elements

The conjugative, chromosomally integrating element R391 is the archetype of the IncJ class of mobile genetic elements. Originally found in a South African Providencia rettgeri strain, R391 carries antibiotic and mercury resistance traits, as well as genes involved in mutagenic DNA repair. While initially described as a plasmid, R391 has subsequently been shown to be integrated into the bacterial chromosome, employing a phage-like integration mechanism closely related to that of the SXT element from Vibrio cholerae O139. Analysis of the complete 89-kb nucleotide sequence of R391 has revealed a mosaic structure consisting of elements originating in bacteriophages and plasmids and of transposable elements. A total of 96 open reading frames were identified; of these, 30 could not be assigned a function. Sequence similarity suggests a relationship of large sections of R391 to sequences from Salmonella, in particular those corresponding to the putative conjugative transfer proteins, which are related to the IncHI1 plasmid R27. A composite transposon carrying the kanamycin resistance gene and a novel insertion element were identified. Challenging the previous assumption that IncJ elements are plasmids, no plasmid replicon was identified on R391, suggesting that they cannot replicate autonomously.

Isolation of a novel Thermus thermophilus metal efflux protein that improves Escherichia coli growth under stress conditions

The mechanisms of metal ion transport in thermophilic organisms are poorly understood. Phage display-based screening of a Thermus thermophilus genomic library in Escherichia coli led to the identification of a novel metal cation efflux protein. The Thermus protein showed extensive sequence and putative structural conservation to Czr and Czc proteins in mesophilic bacterial and mammalian species. Expression of the gene in E. coli led to increased resistance to zinc and cadmium ions, but not to cobalt, in an effect that was apparently caused by increased efflux of metals from the cell. This increased resistance was inducible by zinc and cadmium and, to a lesser extent, by cobalt. Furthermore, E. coli cells containing the Thermus gene exhibited improved cell physiology and delayed cell lysis during recombinant protein production, leading to accumulation of higher levels of recombinant protein. The molecular basis and potential application of the findings are discussed.

Cloning and characterisation of the Hint homologue of the thermophile Thermus thermophilus

Screening of a genomic library of the thermophile Thermus thermophilus revealed a novel thermophilic hint gene, homologues of which are highly conserved in genera from archaea to mammals. Hint belongs to the HIT protein super-family, which contains two broad groups, Fhit, associated with tumour suppression in eukaryotes and Hint with putatitively protein kinase C inhibitory activity. In T. thermophilus the 321 bp gene has a GC content of 67% overall and 94.4% in the third nucleotide position, with unusually no thymine as a wobble base. The gene product, a small highly conserved 11,996 Da predicted soluble cytoplasmic protein, offers an ideal opportunity to investigate thermostabilising amino acid substitutions. Here we report on the characterisation of the novel hint sequence.

Isolation and characterisation of the ylmE homologue of Thermus thermophilus

Screening of a Thermus thermophilus genomic library led to the identification of a homologue of the ylmE gene. ylmE is highly conserved in widely divergent organisms from prokaryotes to mammals, suggesting an important, albeit currently unknown, cellular function. The 633 bp gene has a GC content of 69.2% overall and 90% in the third nucleotide position, while the gene product is predicted to be a soluble cytoplasmic protein of 23,441 Da. It belongs to a family of conserved proteins of unknown function and exhibits amino acid identities ranging from 45% to 28% to the Aquifex aeolicus and Saccharomyces cerevisiae family members, respectively. We speculate that the gene product may be involved in a cellular stress response in T. thermophilus.

Isolation and analysis of a circular form of the IncJ conjugative transposon-like elements, R391 and R997: implications for IncJ incompatibility

The incompatibility between the chromosomally integrating, conjugative transposon-like, IncJ elements R997 (ampicillin resistant) and R391 (kanamycin resistant) was examined by constructing strains harbouring both elements. Unusually, recA(+) strains harbouring the resistance determinants of both elements could be isolated but all strains lacked detectable extrachromosomal DNA. The phenotypic characteristics and transfer patterns observed suggested the formation of recombinant hybrids rather than strains harbouring both elements independently. Formation of strains harbouring two IncJ elements in a recA background was thus examined and resulted in the visualisation of extrachromosomal DNA. When R391 was transferred to a recA strain containing integrated R997, both elements co-existed stably and resulted in the isolation of a plasmid of 93.9 kb. When R997 was transferred to a recA strain harbouring an integrated R391, a plasmid of 85 kb was isolated. Comparison of restriction patterns for both elements revealed many common and several distinct fragments indicating a close physical relationship. These data suggest that although IncJ elements normally integrate at a unique site in the Escherichia coli chromosome, they possess the ability for autonomous replication which becomes manifest in a recA background when this site is occupied. This observation has implications for the nature of the incompatibility associated with IncJ elements and also provides a reliable method for isolating IncJ elements for molecular characterisation.

Influence of sodium oxide content on bioactive glass properties

The rate of in vivo degradation and level of bioactivity of bioactive glasses are composition dependent [1]. By altering bioactive glass composition, the rate of resorption can be controlled. The network connectivity of a glass can be used to predict various physical properties of the glass including its solubility and, hence, its bioactivity [2]. Glass solubility increases as network connectivity is reduced. Glasses in the soda-lime phosphosilicate system were studied. The initial choice of composition was based on phosphate content and low network connectivity. A systematic substitution of calcium oxide for sodium oxide on a molar basis was made in order to examine the influence of sodium oxide content on the glass properties while keeping the network connectivity constant. The glass transition temperature and the peak crystallization temperature were seen to decrease linearly with increasing sodium oxide content. Thermal expansion coefficient and glass density were also seen to be related to sodium oxide content. Preliminary in vitro biocompatibility studies revealed that the glasses of higher sodium oxide content were associated with a cytotoxic response. The measurement of media pH indicated that this cytotoxic effect was due to ion exchange reactions at the glass surface.

Monitoring of chromosomal insertions of the IncJ elements R391 and R997 in Escherichia coli K-12

The integration site(s) of the IncJ element, R391, was localised to a specific region of the Escherichia coli chromosome, between the uxuA and serB loci (98.0-99.5 min), using classical Hfr mapping techniques. F-prime plasmid hosts, diploid for regions spanning the E. coli chromosome, were used as recipients in R391 and R997 conjugal transfer assays. Analysis of transconjugants revealed the integration of R391 and R997 into specific F-primes that contain the uxuA to serB region, but not F-primes that contain other regions of the chromosome. A comparison of the electrophoretic mobility of the original F-primes with those containing inserts demonstrated the integration of large elements, in excess of 85 kb. Linear integration of the IncJ elements into chromosomal DNA was demonstrated in recombination-deficient (recA) backgrounds in the absence of detectable autonomous stages. These observations account for the inability to isolate plasmid DNA from IncJ hosts, and suggests that the elements exhibit a conjugative transposon-like biology in E. coli.

Transfer of the IncJ plasmid R391 to recombination deficient Escherichia coli K12: evidence that R391 behaves as a conjugal transposon

A study of the IncJ plasmid R391 confirmed a low frequency of transfer between recombination proficient (recA+) Escherichia coli (10(-5) donor -1). Reanalysis of its transfer to recombination deficient (recA) E. coli revealed an equivalent transfer frequency to and from all mutants tested. Extrachromosomal DNA could not be detected in either recA+ or recA transconjugants, while R391 proved refractory to curing in both backgrounds implying a high degree of stability. The integration of R391 into a specific region of the chromosome was demonstrated by its transfer as part of the exogenote mobilised from the transfer origins of Hfr strains BW6165 and JC158. Transfer of R391 coupled to recA independent chromosomal integration has significant implications as to the nature and classification of the element. We propose that R391 behaves like a conjugal transposon.

Location and cloning of the ultraviolet-sensitizing function from the chromosomally associated IncJ group plasmid, R391

The IncJ plasmid R391, which specifies a uv-sensitizing function, has been shown to be associated with chromosomal DNA. Deletions originating from Tn10 insertion into the kanamycin-resistance determinant of plasmid R391 gave rise to uv-resistant derivatives. This apparent linkage between the kanamycin-resistance determinant and the uv-sensitizing gene(s) was used to clone the uv-sensitizing function from plasmid R391 into pUR222. A recombinant plasmid containing both functions (KanR and Uvs+) was obtained. The uv-sensitizing function was mapped to a 4-kb EcoRI fragment.

Cloning in Bacillus subtilis of an extremely thermostable alpha amylase: comparison with other cloned heatstable alpha amylases

A heatstable alpha amylase gene was shotgun cloned from Bacillus licheniformis RPO1 into Bacillus subtilis. Restriction endonuclease analysis of the recombinant plasmid revealed a map which was identical to a previously cloned alpha amylase from B. licheniformis FDO2 and very similar to the restriction map of a high temperature amylase from Bacillus coagulans. The thermostability and temperature optimum of the cloned alpha amylase was measureably different from those of the previously reported cloned alpha amylases.

The effect of plasmid R391 and other IncJ plasmids on the survival of Escherichia coli after UV irradiation

The presence of the IncJ plasmids R391, R997, R705, R706, R748 and R749 was shown to sensitize Escherichia coli AB1157 and both its uvrA and lexA derivatives to UV irradiation. No alteration in post-irradiation survival was observed in a recA mutant containing these plasmids, compared with the non-plasmid-containing recA strain. Analysis of recombination frequency in Hfr crosses to recA+ cells containing plasmid R391 indicated a reduction in recombination frequency compared with that obtained in similar crosses to a non-plasmid-containing strain. This effect was not due to plasmid-encoded restriction or entry exclusion systems and therefore must be considered as a real block in recombination. When cells containing plasmid R391 were irradiated and allowed to photoreactivate, an increase in survival was observed which was comparable to that observed in the non-plasmid-containing derivative. This indicated that post-irradiation processing of UV-induced damage, or lack of such processing, by mechanisms other than photoreactivation was responsible for the UV sensitivity associated with plasmid R391.