Restriction map of corynebacteriophages beta c and beta vir and physical localization of the diphtheria tox operon

Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

Background

The human pathogen Corynebacterium diphtheriae is the causative agent of diphtheria. In the 1990s a large diphtheria outbreak in Eastern Europe was caused by the strain C. diphtheriae NCTC 13129. Although the genome was sequenced more than a decade ago, not much is known about its transcriptome. Our aim was to use transcriptome sequencing (RNA-Seq) to close this knowledge gap and gain insights into the transcriptional landscape of a C. diphtheriae tox⁺ strain.

Results

We applied two different RNA-Seq techniques, one to retrieve 5′-ends of primary transcripts and the other to characterize the whole transcriptional landscape in order to gain insights into various features of the C. diphtheriae NCTC 13129 transcriptome. By examining the data we identified 1656 transcription start sites (TSS), of which 1202 were assigned to genes and 454 to putative novel transcripts. By using the TSS data promoter regions recognized by the housekeeping sigma factor σ^A and its motifs were analyzed in detail, revealing a well conserved −10 but an only weakly conserved −35 motif, respectively. Furthermore, with the TSS data 5’-UTR lengths were explored. The observed 5’-UTRs range from zero length (leaderless transcripts), which make up 20% of all genes, up to over 450 nt long leaders, which may harbor regulatory functions. The C. diphtheriae transcriptome consists of 471 operons which are further divided into 167 sub-operon structures. In a differential expression analysis approach, we discovered that genetic disruption of the iron-sensing transcription regulator DtxR, which controls expression of diphtheria toxin (DT), causes a strong influence on general gene expression. Nearly 15% of the genome is differentially transcribed, indicating that DtxR might have other regulatory functions in addition to regulation of iron metabolism and DT. Furthermore, our findings shed light on the transcriptional landscape of the DT encoding gene tox and present evidence for two tox antisense RNAs, which point to a new way of transcriptional regulation of toxin production.

Conclusions

This study presents extensive insights into the transcriptome of C. diphtheriae and provides a basis for future studies regarding gene characterization, transcriptional regulatory networks, and regulation of the tox gene in particular.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4481-8) contains supplementary material, which is available to authorized users.

Biology and molecular epidemiology of diphtheria toxin and the tox gene

Diphtheria toxin (DT) is an extracellular protein of Corynebacterium diphtheriae that inhibits protein synthesis and kills susceptible cells. The gene that encodes DT (tox) is present in some corynephages, and DT is only produced by C. diphtheriae isolates that harbor tox+ phages. The diphtheria toxin repressor (DtxR) is a global regulatory protein that uses Fe2+ as co-repressor. Holo-DtxR represses production of DT, corynebacterial siderophore, heme oxygenase, and several other proteins. Diagnostic tests for toxinogenicity of C. diphtheriae are based either on immunoassays or on bioassays for DT. Molecular analysis of tox and dtxR genes in recent clinical isolates of C. diphtheriae revealed several tox alleles that encode identical DT proteins and multiple dtxR alleles that encode five variants of DtxR protein. Therefore, recent clinical isolates of C. diphtheriae produce a single antigenic type of DT, and diphtheria toxoid continues to be an effective vaccine for immunization against diphtheria.

Molecular basis of vaccination

Vaccines represent the most cost-effective means to prevent infectious diseases. Most of the vaccines which are currently available were developed long before the era of molecular biology and biotechnology. They were obtained following empirical approaches leading to the inactivation or to the attenuation of microorganisms, without any knowledge neither of the mechanisms of pathogenesis of the disease they were expected to protect from, nor of the immune responses elicited by the infectious agents or by the vaccine itself. The past two decades have seen an impressive progress in the field of immunology and molecular biology, which have allowed a better understanding of the interactions occurring between microbes and their hosts. This basic knowledge has represented an impetus towards the generation of better vaccines and the development of new vaccines. In this monograph we briefly summarize some of the most important biotechnological approaches that are currently followed in the development of new vaccines, and provide details on an approach to vaccine development: the genetic detoxification of bacterial toxins. Such an approach has been particularly successful in the rational design of a new vaccine against pertussis, which has been shown to be extremely efficacious and safe. It has been applied to the construction of powerful mucosal adjuvants, for administration of vaccines at mucosal surfaces.

Lysogenic phages of Clostridium perfringens: mapping of the chromosomal attachment sites

The sites of insertion for two lysogenic bacteriophages have been mapped on the chromosome of Clostridium perfringens strain CPN50 using two techniques based on pulsed field gel electrophoresis. Phage phi 29 was mapped to the 1 Mb region of the 3.6 Mb genome, near nanH which encodes a potential virulence factor, while phi 59 was found to have inserted at 2.9 Mb.

Expression of a biologically active diphtheria toxin fragment B in Escherichia coli

The toxB gene of Corynebacterium diphtheriae bacteriophage beta encoding the B fragment of diphtheria toxin was cloned into an inducible expression vector. When expressed in Escherichia coli, fragment B was not proteolysed and was indistinguishable, by immunological criteria, from wild-type C. diphtheriae-derived fragment B. Soluble fragment B was partially purified from the cytoplasm by saline precipitation steps and was shown to compete with the wild-type diphtheria toxin for binding to receptors of sensitive eukaryotic cells. A complete diphtheria toxin was reconstituted by formation of the disulphide bridge between purified fragment A and recombinant fragment B, which migrates at the expected Mr on Western blots and which was able to block protein synthesis by ADP-ribosylation of elongation factor-2, thereby indicating that the recombinant fragment B had retained its biological activity.

Diphtheria-related peptide hormone gene fusions: a molecular genetic approach to chimeric toxin development

There has been considerable effort in chemically conjugating a variety of plant and bacterial toxins to monoclonal antibodies that are directed to surface antigens on target cells. Coupling has been mediated through disulfide linkage, and the resulting conjugates are known generically as immunotoxins. In general, there are a few shortfalls to this approach. For example, since it is clear that not all surface antigens are internalized, one cannot predict the fate of a given IT once bound to its determinant on the surface of a target cell. In addition, in most instances one must activate the amino moiety of lysine residues with a heterobifunctional reagent in order to form disulfide linkage between the ligand and toxophore components. Since the number of reactive groups may be large, the disulfide linked conjugate molecules most likely represent a family of isomeric molecules rather than a defined protein. As a result, one cannot readily manipulate the fine structure of an IT in order to probe the mechanism of toxophore entry into the target cell. The approach that our group has taken toward the development of targeted cytotoxins, however, differs in a fundamental way: Rather than chemically coupling the ligand with toxophore through a disulfide bond, we have turned to genetic engineering in order to create gene fusions whose chimeric products are joined through a peptide bond. Thus, we have genetically constructed a family of fusion genes in which the receptor binding domain of diphtheria toxin has been deleted and replaced with DNAs encoding either alpha-MSH or IL-2. In each instance, it was known that the polypeptide ligand component of the fusion protein bound to specific receptors on target cells and was internalized by receptor mediated endocytosis. We reasoned, therefore, that the substitution of the diphtheria toxin receptor binding domain by these ligands should result in the formation of 'new' toxins whose action should be targeted toward selected eukaryotic cells that expressed either the alpha-MSH or IL-2 receptor. As along as the ligand component was exposed on the surface of the chimeric toxin, the molecule should bind to its receptor and be drawn into the cell by receptor-mediated endocytosis. Since the toxin-related/peptide hormone fusion protein is the product of a chimeric gene, it is a single molecular species. This has allowed us to begin to probe by site-directed mutagenesis the structure of fragment B sequences that are required to facilitate the translocation of fragment A across the target cell membrane.(ABSTRACT TRUNCATED AT 400 WORDS)

DNA element of Corynebacterium diphtheriae with properties of an insertion sequence and usefulness for epidemiological studies

The segment of DNA which is inserted within the tox gene of bacteriophage gamma and is responsible for its Tox- phenotype was found to be present and repeated approximately 30 times in the chromosome of Corynebacterium diphtheriae Belfanti 1030. Other C. diphtheriae strains contained a variable number of copies (1 to 25) of the same element. Sequence analysis showed that this repeated and interspersed DNA element was flanked by 9-base-pair direct repeats and that the 5' and 3' ends of the insertion contained sequences forming an imperfect inverted repeat. Therefore, the DNA segment here described has most of the typical structural features of a bacterial insertion sequence element. We show that different C. diphtheriae isolates derived from the same outbreak of diphtheria have an identical genomic distribution of this DNA element and that such DNA can be useful for epidemiological studies.

Genetic construction, expression, and melanoma-selective cytotoxicity of a diphtheria toxin-related alpha-melanocyte-stimulating hormone fusion protein

The structural gene for diphtheria toxin, tox, has been modified at its Sph I site by the introduction of an oligonucleotide linker encoding a unique Pst I restriction endonuclease site and a synthetic oligonucleotide encoding alpha-melanocyte-stimulating hormone (alpha-MSH). The resulting fusion gene directs the expression of a diphtheria toxin-related alpha-MSH hybrid protein in which the diphtheria toxin receptor-binding domain has been replaced with alpha-MSH sequences. The chimeric toxin has been partially purified from periplasmic extracts of recombinant Escherichia coli K-12 and has been found to be selectively toxic for alpha-MSH receptor-positive human malignant melanoma NEL-M1 cells in vitro.

Characterization of the diphtheria tox transcript in Corynebacterium diphtheriae and Escherichia coli

Transcription of the tox gene in lysogenic Corynebacterium diphtheriae strains C7(beta tox+), C7 (gamma tox) and the hypertoxigenic PW8 (omega tox+) was analyzed and compared with transcription of the C. diphtheriae tox gene in the recombinant strain Escherichia coli (pDT201). In all cases S1 nuclease mapping localized the 5' terminus of the tox mRNA to a site 8 or 9 base pairs (bp) downstream of a region similar to the -10 consensus sequence of E. coli promoters. In C. diphtheriae the tox transcript was observed only in strains that were grown under iron-limiting conditions; in the presence of excess iron, transcription beyond bp 38 of the tox coding region was not observed. In contrast, in E. coli(pDT201) tox was expressed at equivalent levels in both iron-depleted and iron-supplemented media. The DNA insertion in the tox gene of the nontoxigenic corynephage gamma was found to occur at bp 54 of the tox coding region. The insertion event resulted in the duplication of a 7-bp target sequence, and the ends of the insert were found to constitute an imperfect inverted repeat of approximately 26 bp. Transcription from the tox promoter in C7(gamma tox) was found to initiate at the same nucleotides as in C7(beta tox+), PW8, and E. coli(pDT201) and remained sensitive to iron inhibition. These observations are discussed in relation to the mechanism of iron-mediated regulation of the tox gene.

Bacterial toxin vaccines

A rebirth of interest and activity in vaccine development has occurred in recent years which is probably due to the persistence of threat to health by infectious diseases, as well as technological advances which have made possible new approaches to solve old problems. Most work being done today with vaccine development against diseases caused entirely or in part by bacterial toxins falls into the categories of, attenuated organisms (whether by classical means or application of newly developed genetic technologies), and/or toxin subunits (derived by genetic manipulations, peptide synthesis, or chemical modification of toxins). This review discusses some of these new approaches in general as well as specific examples of their application to several bacterial diseases whose pathologies involve toxins.

Detection and physical map of a omega tox+-related defective prophage in Corynebacterium diphtheriae Belfanti 1030(-)tox-

A library of chromosomal DNA from Corynebacterium diphtheriae Belfanti 1030(-)tox- was cloned in the lambda phage vector EMBL4 and screened for sequences homologous to corynephage omega tox+ and the attB1-attB2 region of the C7(-)tox- chromosome. Two portions of the 1030(-)tox- chromosome, 35 and 30.5 kilobases long which contain, respectively, the entire region homologous to corynephage omega tox+ and the attB1-attB2 sites, were mapped with the restriction endonucleases BamHI and EcoRI. Chromosomal DNA from 1030(-)tox- was shown to contain a 15.5-kilobase region that was homologous to ca. 42% of the corynephage omega tox+ genome. These sequences were found to hybridize to three regions of the phage genome and do not contain either the diphtheria tox operon or the attP site. These sequences are distant from the chromosomal region that contains the attB1-attB2 sites. Moreover, unlike other known defective prophages, the physical map of this prophage starts at the cos site and is colinear with the vegetative phage map. The 30.5-kilobase region of the 1030(-)tox- chromosome, which contains the attB1-attB2 sites, has a central core region that is almost identical to the corresponding region of the C7(-)tox- chromosome; however, the flanking sequences in these two strains of C. diphtheriae are different.

Conversion by corynephages and its role in the natural history of diphtheria

The conversion of non-toxinogenic Corynebacterium diphtheriae to toxinogeny has been reviewed. The biology of converting phage and the relationship of converting phages to nonconverting phages are summarized. The significance of these findings to the natural history and evolution of diphtheria is assessed.

Nucleotide sequence of the structural gene for diphtheria toxin carried by corynebacteriophage beta

A 1,942-base-pair DNA segment encoding the structural gene for diphtheria toxin was sequenced, and the primary structure of the toxin was deduced. Restriction enzyme fragments corresponding to nontoxic or hypotoxic peptides of the toxin were isolated from corynebacteriophage beta and cloned into Escherichia coli on plasmid pBR322, and the sequence was determined. The mature toxin molecule deduced from the sequence has 535 amino acid residues and a molecular weight of 58,342. The deduced sequence for the fragment A moiety was the same as that determined at the protein level, except for a single serine residue, which had been mispositioned in the earlier study. Several differences were noted with respect to the partial sequence data available on the fragment B moiety, some or all of which may reflect genetic variations among populations of corynephages carrying the toxin gene. The DNA sequence predicts a 25-residue leader peptide preceding the mature protein, which is presumably involved in secretion of the toxin from lysogenized Corynebacterium diphtheriae. We infer that initiation of translation probably occurs at a GTG codon (codon -25). Cloned restriction fragments containing sequences for the amino-terminal region of toxin, together with 5' flanking regions, were expressed in E. coli. Toxin-related peptides were synthesized and secreted into the periplasmic space. These results provide a basis for applying recombinant DNA methods to the study of diphtheria toxin and for producing novel, genetically altered forms of the toxin suited to the construction of new classes of immunotoxins.

Molecular cloning and expression of gene fragments from corynebacteriophage beta encoding enzymatically active peptides of diphtheria toxin

Two restriction fragments from corynebacteriophage beta vir tox+ that encode peptides similar to diphtheria toxin fragment A and the chain termination fragment, CRM45, have been cloned into Escherichia coli in plasmid pBR322. Clones containing the recombinant plasmids produced gene products that were active in catalyzing the ADP ribosylation of elongation factor 2 and were reactive with diphtheria toxin antiserum. Toxin-related peptides were found primarily in the periplasmic compartment and were degraded to nonimmunoreactive forms within 1 to 2 h of synthesis. The expression of both gene fragments appears to have originated from the diphtheria toxin promoter.

Studies on the molecular epidemiology of diphtheria

DNA was extracted from toxigenic and nontoxigenic (tox+ and tox-) diphtheria bacilli isolated during a carrier survey that followed recovery of a tox+ Corynebacterium diphtheriae mitis from a baby with membranous tonsillitis. The electrophoretic gel patterns of restriction enzyme digests were indistinguishable from one another. They were, however, readily distinguishable from similar gels of DNAs extracted from diphtheria bacilli associated with outbreaks elsewhere. Hybridisation of a labelled nick-translated corynephage-beta c-DNA probe to nitrocellulose blots of these gels occurred only to blots from tox+ strains. Other hybridisation studies showed that all of seven strains, each isolated from a diphtheria case or carrier in a different part of the world, carried a prophage with DNA closely related to phage beta tox+. When an individual carrying a tox+ diphtheria bacillus arrives in an immunised community, spread of the tox gene to other individuals may be via phage conversion of tox- C diphtheriae already prevalent among the nasopharyngeal bacterial flora of the local populace, rather than by colonisation with the tox+ strain itself.

The complete nucleotide sequence of the gene coding for diphtheria toxin in the corynephage omega (tox+) genome

A segment of corynephage omega (tox+) DNA, containing the gene for diphtheria toxin (tox) was fragmented with restriction enzymes and the fragments cloned into M13 vectors for nucleotide sequence determination. A long open reading frame was shown to encode the tox gene by comparing the predicted amino acid sequence with that of peptides derived from the mature toxin molecule. Analysis of the nucleotide sequence shows RNA polymerase and ribosome binding signals preceding a GTG codon in the open reading frame: if this is the correct starting signal for translation, then a 25 amino acid signal peptide can be predicted for the toxin molecule.

Molecular epidemiological studies of United States Gulf Coast Vibrio cholerae strains: integration site of mutator vibriophage VcA-3

Environmental and clinical Vibrio cholerae O-1 strains isolated from the U.S. Gulf Coast region were found to be lysogenic for a vibriophage which we have designated VcA-3. Comparison of VcA-3 with the previously described vibriophages VcA-1 and VcA-2 has shown that VcA-1 and VcA-3 are homoimmune, have extensive sequence homology, but have markedly different restriction endonuclease digestion patterns. VcA-3 was found to randomly integrate into the V. cholerae RV79 chromosome and to introduce stable auxotrophic mutations. We show that all U.S. Gulf Coast environmental and clinical isolates that are lysogenic for VcA-3, including both tox+ and tox- isolates, contain the prophage integrated at an identical chromosomal site. Given the known stability of temperate mutator bacteriophages, these results suggest that there is a clonal relationship among the V. cholerae O-1 strains examined in this study, including the tox+ and tox- isolates.

Detection and expression of DNA homologous to the tox gene in nontoxinogenic isolates of Corynebacterium diphtheriae

Three probes have been described which can be used to detect the presence of DNA sequences homologous to the tox gene of Corynebacterium diphtheriae. Probes "A" and "B" detected sequences coding for A and B fragments of diphtheria toxin, respectively. The third "A-B" probe contained both the A and B coding sequences. The B probe was completely unambiguous in detecting only toxin-related sequences, and the A probe was only slightly less so. The efficacy of the probes was tested on a series of toxinogenic and nontoxinogenic isolates of C. diphtheriae. All isolates which were toxinogenic as characterized by the gel immunodiffusion technique gave positive reactions with the probes. Of particular interest was the finding that 14 of 43 nontoxinogenic isolates also carried DNA homologous to both the A and B probes. All 14 isolates were nontoxinogenic by the rabbit intracutaneous test as well as by the gel immunodiffusion test; however, 12 of them produced ADP-ribosylating activity, whereas two were negative. The isolates producing ADP-ribosylating activity belonged to a cohort of cultures, of which 11 were isolated in South Dakota and 1 was isolated in Montana. Genomic DNAs of all 12 appeared to be identical when restriction enzyme digest patterns were compared, and the same fragment carried the tox gene in all of them. The tox-bearing nontoxinogenic isolates from Alaska and Florida each had unique restriction patterns and did not produce ADP-ribosylating activity. A number of genomic fragments of all the tox-bearing nontoxinogenic isolates hybridized with beta converting phage DNA. The significance of these observations to the natural history of diphtheria was discussed.

Nucleotide sequence and expression of the diphtheria tox228 gene in Escherichia coli

The complete nucleotide sequence of the diphtheria tox228 gene encoding the nontoxic serologically related protein CRM228 has been determined. A comparison of the predicted amino acid sequence with the available amino acid sequences from the wild-type toxin made it possible to deduce essentially the entire nucleotide sequence of the wild-type tox gene. The signal peptide of pro-diphtheria toxin and the putative tox promoter have been identified, a highly symmetrical nucleotide sequence downstream of the toxin gene has been detected; this region may be the corynebacteriophage beta attachment site (attP). The cloned toxin gene was expressed at a low level in Escherichia coli.

Cloned fragment A of diphtheria toxin is expressed and secreted into the periplasmic space of Escherichia coli K12

An 831-base pair segment of the corynebacteriophage beta tox-45 genome encoding fragment A of diphtheria toxin was cloned into plasmid pUC8 in Escherichia coli K12. Strains containing recombinant plasmids expressed the adenosine diphosphate ribosyl transferase activity characteristic of fragment A; this activity could be inhibited by polyvalent antiserum to fragment A as well as by the appropriate monoclonal antibodies to diphtheria toxin. The transferase activity was secreted into the periplasmic space of E. coli. These findings have implications for the future construction of genetically engineered chimeric toxins.

Integration of corynebacteriophages beta tox+, omega tox+, and gamma tox- into two attachment sites on the Corynebacterium diphtheriae chromosome

The bacterial attachment sites of independently isolated Corynebacterium diphtheriae strains C7s and (belfanti)1030 lysogenic for corynebacteriophages beta tox+, omega tox+, and gamma tox- were determined by Southern blot analysis. Both corynebacterial strains contained two distinct bacterial attachment sites (attB1 and attB2). We found that infection by any of the three closely related corynebacteriophages may give rise to single, double, and triple lysogens. In the case of toxigenic C. diphtheriae strains C7s(beta tox+) and C7s(omega tox+), the final yields of diphtheria toxin produced under optimal conditions were equivalent and varied by one-, two-, or threefold depending upon the number of integrated prophage.

Restriction endonuclease map of corynebacteriophage omega ctox+ isolated from the Park-Williams no. 8 strain of Corynebacterium diphtheriae

The toxigenic corynebacteriophage omega tox+ was isolated from the hypertoxigenic Park-Williams no. 8 (PW8) strain of Corynebacterium diphtheriae and compared with the toxigenic corynebacteriophage beta tox+. The physical size and host range of both phages were found to be identical. An endonuclease restriction map of omega tox+ was constructed, and the locations of the cohesive ends (cos), phage attachment site (attP), and the diphtheria tox operon were identified. The genome of omega tox+ was found to differ from that of beta tox+ in three regions. In addition, omega tox+ was shown to be integrated into two nontandem corynebacterial phage attachment sites (attB1, attB2) in the PW8 chromosome. The differences in the restriction endonuclease digestion maps of omega tox+ and beta tox+ and the contribution of double lysogeny are discussed in relation to the hypertoxigenicity of the PW8 strain.

Restriction endonuclease map of the nontoxigenic corynephage gamma c and its relationship to the toxigenic corynephage beta c

Clear-plaque-forming mutant gamma tox- corynephages were isolated independently from nontoxigenic lysogenic Corynebacterium diphtheriae strains C7s(gamma tox-) and C4(gamma tox-). A physical map was constructed by using restriction endonucleases BamHI, EcoRI, HindIII, and KpnI. A comparison of nontoxigenic gamma c with toxigenic corynephage beta c revealed large areas of homology, including common regions for cohesive ends (cos) and attachment sites (att). Localization of the att sites on the beta prophage and correlation of the physical and genetic maps defined the orientation of the diphtheria tox operon. Diphtheria tox sequence homologies were mapped on gamma c by hybridizing 32P-labeled diphtheria tox mRNA to restriction fragments of gamma c DNA. Two regions of heterogeneity between phages beta c and gamma c were localized and these regions accounted for the 3-kilobase larger molecular size of gamma c compared with beta c. One change occurs near the tox promoter and may explain the nontoxigenic phenotype of corynephage gamma tox-.

Identification of deoxyribonucleic acid restriction fragments of beta-converting corynebacteriophages that carry the gene for diphtheria toxin

Deoxyribonucleic acid fragments bearing the gene for diphtheria toxin have been identified in restriction enzyme digests of deoxyribonucleic acids from beta-converting and gamma-nonconverting corynebacteriophages. A combination of physical and genetic evidence has established that the Bam HI band C fragment of beta phage deoxyribonucleic acid, which carries the specific phage attachment site (Buck and Groman, J. Bacteriol. 148:131-142, 1981), also carries most, and probably all, of the gene for diphtheria toxin. A detailed restriction map of this tox-bearing Bam HI fragment has been developed, and the locations and orientation of the tox gene and the attP site within this fragment have been established.