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Use of Tn KPK2 for sequencing a 10.6-kb PstI DNA fragment of Bradyrhizobium japonicum and for the construction of aspA and ndvA mutants.

Transposon Tn KPK2 was used to saturate a randomly cloned Bradyrhizobium japonicum PstI fragment and the insertions were used as starting points for the sequence determination. The first gene of the 10.6-kb DNA insert encodes a homologue to ndvA, the product of which is known to be involved in the formation of periplasmic cyclic glucans. Selected Tn KPK2 insertions were introduced into the B. japonicum wild-type strain. The resulting mutants were subsequently tested for their symbiotic interactions with soybeans. As in Sinorhizobium meliloti, a B. japonicum ndvA mutant was affected in salt-stress tolerance and exhibited symbiotic defects in that it induced the formation of ineffective soybean nodules. The central nodule tissue was infected by bacteroids, but within the infected cells the mutant was not properly maintained. Another gene was found to be highly similar to bacterial aspartases and thus was named aspA. The putative function of the product of this gene was confirmed by genetic complementation of aspartase-less Escherichia coli strain TK237. The symbiotic phenotype of a B. japonicum aspA:Tn KPK2 mutant consisted of enlarged symbiosomes that made the system ineffective. In general, Tn KPK2 is a suitable means for fast sequencing. In combination with pJQ200SK, the resulting recombinant plasmids can be directly used to create genetically defined mutants.

ATP-Binding Cassette Transporters↗

Hypervirulence-associated pseudo-compound transposons as fundamental mobile units driving cross-species virulence dissemination in Enterobacteriaceae.

BACKGROUND: The rapid global spread of hypervirulence in Enterobacteriaceae, particularly in carbapenem-resistant Klebsiella pneumoniae, poses a significant public health threat. However, the key genetic vehicles and mechanisms driving horizontal transfer of hypervirulence-associated genes (iucA, iroB, rmpA, rmpA2, and peg-344) remain poorly defined, limiting effective surveillance. METHODS: We performed a large-scale genomic survey of 2,869 virulence-associated plasmid sequences and 2,337 complete Enterobacteriaceae chromosomes. Using comparative genomics and evolutionary analyses, we systematically identified and characterized Hypervirulence-associated Pseudo-Compound Transposons (Hva-PCTs), defined as structured mobile elements in which hypervirulence-associated genes are flanked by insertion sequences. RESULTS: Our results demonstrate that hypervirulence-associated genes are transmitted primarily as discrete IS-bounded units, which we term Hva-PCTs. We identified 29 distinct plasmid-borne Hva-PCTs (pHva-PCTs) and 30 chromosomal Hva-PCTs (cHva-PCTs). These modules show clear species-specific patterns: iucA/iroB-associated Hva-PCTs mainly originate in Escherichia coli and spread through IncFIB-containing multi-replicon plasmids (commonly combined with IncFIC(FII) and/or IncFII, while rmpA/rmpA2/peg-344-containing modules originate in K. pneumoniae and are disseminated via IncHI1B/repB plasmids. Three Hva-PCTs were detected on both plasmids and chromosomes (xHva-PCTs). In one clinical K. pneumoniae isolate (LS356), the identical composite module was present on both replicons. Simpler sub-modules, such as ISKqu3-rmpA2-iucA_1-IS102 and IS102-rmpA-peg-344-iroB_1-IS1A, frequently co-occur on the same plasmid; when positioned in tandem, they reconstitute the full composite structure. This assembly pattern is further supported by a partial duplication event in plasmid pP901. CD-HIT clustering (80% nucleotide identity and 90% coverage) showed that 13 of 22 major clusters contained both plasmid and chromosomal copies, with intra-cluster identities >80% across multiple sequence types and host species. CONCLUSION: Hypervirulence-associated genes in Enterobacteriaceae are disseminated mainly as IS-flanked Hva-PCTs rather than solely through intact virulence plasmids. These modules exhibit strong but not absolute host specificity. The presence of identical Hva-PCTs on plasmids and chromosomes suggests inter-replicon mobility, while their stepwise assembly from simpler sub-modules highlights modular accretion as a key evolutionary process. Tracking Hva-PCTs as distinct mobile units may complement existing plasmid- and gene-centric surveillance approaches for hypervirulent and convergent strains. Experimental validation of their transposition activity and phenotypic effects is still required.

Virulence↗

SfiI genomic cleavage map of Escherichia coli K-12 strain MG1655.

An SfiI restriction map of Escherichia coli K-12 strain MG1655 is presented. The map contains thirty-one cleavage sites separating fragments ranging in size from 407 kb to 3.7 kb. Several techniques were used in the construction of this map, including CHEF pulsed field gel electrophoresis; physical analysis of a set of twenty-six auxotrophic transposon insertions; correlation with the restriction map of Kohara and coworkers using the commercially available E. coli Gene Mapping Membranes; analysis of publicly available sequence information; and correlation of the above data with the combined genetic and physical map developed by Rudd, et al. The combination of these techniques has yielded a map in which all but one site can be localized within a range of +/- 2 kb, and over half the sites can be localized precisely by sequence data. Two sites present in the EcoSeq5 sequence database are not cleaved in MG1655 and four sites are noted to be sensitive to methylation by the dcm methylase. This map, combined with the NotI physical map of MG1655, can aid in the rapid, precise mapping of several different types of genetic alterations, including transposon mediated mutations and other insertions, inversions, deletions and duplications.

Base Sequence↗

Characterization of a Staphylococcus aureus transposon, Tn5405, located within Tn5404 and carrying the aminoglycoside resistance genes, aphA-3 and aadE.

A new staphylococcal composite transposon, designated Tn5405, carrying the genes aphA-3 and aadE, which encode resistance to aminoglycosides, was partially characterized. The transposon is 12 kb long and is flanked by inverted repeated sequences displaying the characteristic features of an insertion sequence, named IS1182. This insertion sequence is 1864 bp long and has 23/33-bp imperfect inverted repeats at its ends. One of the IS1182 copies delimiting Tn5405 contains a copy of IS1181 flanked by 8-bp direct repeats. Tn5405 was found in the chromosome of MRSA clinical isolate BM3121, within a Tn552-related transposon, Tn5404. Tn5404 was previously characterized following its transposition onto a beta-lactamase plasmid harbored by BM3121. Two forms of the recombinant beta-lactamase-encoding plasmid generated by the inversion of Tn5405 within Tn5404 were detected. IS1182 was not detected in the DNA of 4 of the 17 tested MRSA isolates containing aphA-3 and resistant to streptomycin. Thus, aphA-3 and aadE genes are not disseminated only by Tn5405 or related transposons delimited by IS1182.

Amino Acid Sequence↗

Sequence analysis of termini of conjugative transposon Tn916.

Transposon Tn916 is a 16.4-kilobase, broad-host-range, conjugative transposon originally identified on the chromosome of Enterococcus (Streptococcus) faecalis DS16. Its termini have been sequenced along with the junction regions for two different insertions. The ends were found to contain imperfect inverted repeat sequences with identity at 20 of 26 nucleotides. Further in from the ends, imperfect directly repeated sequences were present, with 24 of 27 nucleotides matching. The transposon junction regions contained homologous segments but of a nature not consistent with a direct duplication of the target sequence. Within the right terminus was a potential outwardly reading promoter. Tn916 is believed to transpose via an excision-insertion mechanism; based on the analyses of the termini, as well as two target sequences (before insertion and after excision), a possible model is suggested.

Base Sequence↗

Sequence analysis of a functional Drosophila centromere.

Centromeres are the site for kinetochore formation and spindle attachment and are embedded in heterochromatin in most eukaryotes. The repeat-rich nature of heterochromatin has hindered obtaining a detailed understanding of the composition and organization of heterochromatic and centromeric DNA sequences. Here, we report the results of extensive sequence analysis of a fully functional centromere present in the Drosophila Dp1187 minichromosome. Approximately 8.4% (31 kb) of the highly repeated satellite DNA (AATAT and TTCTC) was sequenced, representing the largest data set of Drosophila satellite DNA sequence to date. Sequence analysis revealed that the orientation of the arrays is uniform and that individual repeats within the arrays mostly differ by rare, single-base polymorphisms. The entire complex DNA component of this centromere (69.7 kb) was sequenced and assembled. The 39-kb "complex island" Maupiti contains long stretches of a complex A+T rich repeat interspersed with transposon fragments, and most of these elements are organized as direct repeats. Surprisingly, five single, intact transposons are directly inserted at different locations in the AATAT satellite arrays. We find no evidence for centromere-specific sequences within this centromere, providing further evidence for sequence-independent, epigenetic determination of centromere identity and function in higher eukaryotes. Our results also demonstrate that the sequence composition and organization of large regions of centric heterochromatin can be determined, despite the presence of repeated DNA.

Animals↗

Heterochromatin-based silencing of a foreign tandem repeat in Drosophila melanogaster shows unusual biochemistry and temperature sensitivity.

Eukaryotic genomes are packaged into chromatin, a regulatory nucleoprotein assembly. Establishment, maintenance, and interconversion of chromatin states is required for correct patterns of gene expression, genome integrity, and survival. Transcriptionally repressive heterochromatin minimizes mobilization of transposable elements and limits expansion of other repetitive DNA, but mechanisms for recognition of the latter sequences are not well established. We previously demonstrated in Drosophila melanogaster that transcripts derived from 1360 and Invader4 transposon insertions can trigger local conversion of transcriptionally permissive euchromatin to heterochromatin through the piRNA system, but only in a subset of genomic locations near existing blocks of heterochromatin. Here we show that a ~9 kb tandem array of the 36-nucleotide lac operator (lacO) sequence of Escherichia coli can form ectopic heterochromatin at a similar subset of sites, resulting in variegating expression of an adjacent reporter gene. Heterochromatin Protein 1a (HP1a) and histone deacetylation are required for lacO repeat-induced silencing, but, contrasting with previously described Position Effect Variegation (PEV), we do not observe increased histone H3 lysine 9 methylation. Silencing is effective at 25°C and suppressed at 18°C (in contrast to canonical PEV, which is enhanced at 18°C), indicating involvement of a temperature-sensitive component. Temperature switching experiments show that lacO repeat-induced heterochromatin formation is reversible throughout larval development following an HP1a-dependent initiation step in the early embryo. We conclude that the Drosophila nucleus can recognize a completely foreign tandem repeat as a target for heterochromatin formation, and that the heterochromatin structure established is distinct from that of endogenous tandem arrays.

HP1a↗

A genetic approach to demonstrate the role of listeriolysin O in the virulence of Listeria monocytogenes.

The locus of insertion of a transposon previously used to obtain a non-haemolytic avirulent mutant was identified: it is the structural gene encoding lisreriolysin O, the thiol-dependent haemolysin, now called hlyA. The gene was completely sequenced. The preliminary structural and functional study of the chromosomal region containing the gene indicates that hlyA belongs to a monocistronic transcriptional unit. If it is the case, the transposon insertion would have no major polar effect on downstream genes and would only affect hlyA expression. These results emphasize the importance of the haemolysin in the virulence of Listeria monocytogenes.

Amino Acid Sequence↗

Inactivation of maize transposon Mu suppresses a mutant phenotype by activating an outward-reading promoter near the end of Mu1.

We described previously a mutation in maize, hcf106, caused by the insertion of a Mu1 transposon. When the Mu transposon system is in an active phase, hcf106 conditions a nonphotosynthetic, pale green phenotype. However, when the Mu system is inactive (a state correlated with hypermethylation of Mu elements), the plant adopts a normal phenotype despite the continued presence of the transposon within the gene. The molecular mechanisms that mediate this suppression of the mutant phenotype have now been investigated. We show here that the Mu element responsible for the hcf106 lesion lies within sequences encoding the 5'-untranslated leader of the Hcf106 mRNA. When the Mu transposon system is active, this insertion interferes with the accumulation of mRNA from the hcf106 allele. However, when Mu is inactive, mRNA similar in size and abundance to that transcribed from the normal allele accumulates. These transcripts initiate at many sites throughout a 70-base-pair region, within and immediately downstream of the Mu1 insertion. Thus, an unusual promoter spanning the downstream junction between Mu1 and Hcf106 substitutes for the normal Hcf106 promoter but only when Mu is inactive. The pattern of mRNA accumulation in different organs and in response to light suggests that the activity of this promoter is conditional not only upon the phase of Mu activity, but also upon signals that regulate the normal Hcf106 promoter.

Base Sequence↗

A new example of physical linkage between Tn1 and Tn21: the antibiotic multiple-resistance region of plasmid pCFF04 encoding extended-spectrum beta-lactamase TEM-3.

The genetic environment of plasmid-borne blaTEM mutant genes, encoding nine distinct TEM-type extended-spectrum beta-lactamases, was studied in transconjugants from clinical isolates of enterobacteria. Colony hybridization with probes specific for tnpA and tnpR of Tn3, tnpA and tnpI of Tn21, aacA4, and IS15, and restriction endonuclease analysis of plasmid DNA indicated that the structural genes for the enzymes were always associated with intact or deleted variants of the Tn3 family. Four of the nine blaTEM variants, which account for 62% of 222 isolates in a molecular epidemiological study, were associated with replicons indistinguishable from the epidemic Inc7-M plasmid pCFF04 that carries the blaTEM-3 gene. This suggests that mutant genes were selected from the same prototype plasmid carrying penicillinase genes blaTEM-1 or -2. A 6.6 kb DNA fragment of pCFF04 containing blaTEM-3 was characterized by amplification mapping and sequencing. The results obtained indicated that blaTEM-3 was present on a copy of Tn1 interrupted at the start codon of the transposase by a DNA sequence reminiscent of the inverted repeats of class II transposons. This partial Tn1 copy was in turn, inserted into the transposase gene of a Tn21-like transposon containing an integron expressing an aacA4 gene. The presence of an integron can account for the various assortments of aminoglycoside resistance genes found associated with blaTEM-3.

Amino Acid Sequence↗

An E. coli DNA fragment 118 base pairs in length provides dnaY+ complementing activity.

The dnaY gene of E. coli, thought to be involved in the polymerization phase of DNA replication, was localized on a fragment 118 base pairs in length. This fragment, cloned in two different vectors and tested in a dnaY (Ts) recA host, has dnaY + complementing activity. The nucleotide sequence of the 118 base pairs and flanking bases was determined. The dnaY complementing activity was inactivated by transposon insertion and by localized chemical mutagenesis. Three independent insertions of Tn5 into the 118 base pair region eliminated dnaY activity. Eight single-base-change mutations that resulted in loss of dnaY activity also were located within the 118 base pair region. Analysis of the nucleotide sequence reveals a potential promoter but reveals no open reading frames likely to be translated into polypeptides. However, an RNA transcript of the dnaY region is synthesized in vivo. Perhaps the active product of dnaY is a small RNA or perhaps the dnaY region functions as a site.

Base Composition↗

Rapid sequence turnover at an intergenic locus in Drosophila.

Closely related species of Drosophila tend to have similar genome sizes. The strong imbalance in favor of small deletions relative to insertions implies that the unconstrained DNA in Drosophila is unlikely to be passively inherited from even closely related ancestors, and yet most DNA in Drosophila genomes is intergenic and potentially unconstrained. In an attempt to investigate the maintenance of this intergenic DNA, we studied the evolution of an intergenic locus on the fourth chromosome of the Drosophila melanogaster genome. This 1.2-kb locus is marked by two distinct, large insertion events: a nuclear transposition of a mitochondrial sequence and a transposition of a nonautonomous DNA transposon DNAREP1_DM. Because we could trace the evolutionary histories of these sequences, we were able to reconstruct the length evolution of this region in some detail. We sequenced this locus in all four species of the D. melanogaster species complex: D. melanogaster, D. simulans, D. sechellia, and D. mauritiana. Although this locus is similar in size in these four species, less than 10% of the sequence from the most recent common ancestor remains in D. melanogaster and all of its sister species. This region appears to have increased in size through several distinct insertions in the ancestor of the D. melanogaster species complex and has been shrinking since the split of these lineages. In addition, we found no evidence suggesting that the size of this locus has been maintained over evolutionary time; these results are consistent with the model of a dynamic equilibrium between persistent DNA loss through small deletions and more sporadic DNA gain through less frequent but longer insertions. The apparent stability of genome size in Drosophila may belie very rapid sequence turnover at intergenic loci.

Animals↗

Cloning and expression in Escherichia coli of the streptolysin O determinant from Streptococcus pyogenes: characterization of the cloned streptolysin O determinant and demonstration of the absence of substantial homology with determinants of other thiol-activated toxins.

A gene bank of Streptococcus pyogenes Richards was constructed in Escherichia coli by using the bacteriophage replacement vector lambda L47.1, and hybrid phage expressing streptolysin O (SLO) were identified among the recombinants. DNA sequences encoding SLO were subcloned from an slo+ hybrid phage into a low-copy-number vector plasmid to yield an slo+ hybrid plasmid, pMK157. This plasmid contains 5.6 kilobase pairs of cloned streptococcal DNA sequences, is stable, and expresses SLO at easily detectable levels in E. coli. Transposon gamma delta insertion mutants and in vitro-generated deletion mutants of pMK157 were isolated and analyzed. This analysis showed that a single gene is sufficient for production of SLO in E. coli and allowed this slo gene to be mapped to within +/- 100 base pairs. Two forms of the slo gene product, with molecular weights of 68,000 and 61,000, were detected in E. coli minicells harboring slo+ plasmids and by immunoblotting of E. coli whole cells harboring slo+ plasmids. Southern blotting hybridization experiments with the cloned SLO DNA sequences as probes failed to demonstrate homology between the cloned SLO determinant and DNA isolated from bacteria expressing thiol-activated cytolysins related to SLO.

Bacterial Proteins↗

A homologue of the recombination-dependent growth gene, rdgC, is involved in gonococcal pilin antigenic variation.

Neisseria gonorrhoeae pilin undergoes high-frequency changes in primary amino acid sequence that aid in the avoidance of the host immune response and alter pilus expression. The pilin amino acid changes reflect nucleotide changes in the expressed gene, pilE, which result from nonreciprocal recombination reactions with numerous silent loci, pilS. A series of mini-transposon insertions affecting pilin antigenic variation were localized to three genes in one region of the Gc chromosome. Mutational analysis with complementation showed that a Gc gene with sequence similarity to the Escherichia coli rdgC gene is involved in pilus-dependent colony phase variation and in pilin antigenic variation. Furthermore, we show that the Gc rdgC homologue is transcriptionally linked in an operon with a gene encoding a predicted GTPase. The inability to disrupt expression of this gene suggests it is an essential gene (engA, essential neisserial GTPase). While some of the transposon mutations in rdgC and insertions in the 5'-untranslated portion of engA showed a growth defect, all transposon insertions investigated conferred an aberrant cellular morphology. Complementation analysis showed that the growth deficiencies are due to the interruption of RdgC expression and not that of EngA. The requirement of RdgC for efficient pilin variation suggests a role for this protein in specialized DNA recombination reactions.

Amino Acid Sequence↗

Lipopolysaccharide dependence of cyanophage sensitivity and aerobic nitrogen fixation in Anabaena sp. strain PCC 7120.

Fox- mutants of Anabaena sp. strain PCC 7120 are unable to fix dinitrogen in the presence of oxygen. A fragment of the DNA of Anabaena sp. was cloned by complementation of a spontaneous Fox-, cyanophage-resistant mutant, R56, and characterized. Random insertion of transposon Tn5 delimited the complementing DNA to a 0.6-kb portion of the cloned fragment. Sequencing of this region and flanking DNA showed one complete open reading frame (ORF) similar to the gene rfbP (undecaprenyl-phosphate galactosephosphotransferase) and two partial ORFs similar to genes rfbD (GDP-D-mannose dehydratase) and rfbZ (first mannosyl transferase), all of which are active in the synthesis of the O antigen unit of the lipopolysaccharide (LPS) component of the outer membrane of gram-negative bacteria. In a transposon (Tn5-1087b)-induced, Fox-, cyanophage-resistant mutant, B14, the transposon was found within the same rfbP-like ORF. The three ORFs were insertionally inactivated with the omega cassette (P. Prentki and H. M. Krisch, Gene 29:303-313, 1984) or with Tn5::omega. Only the insertions in the rfbZ- and rfbP-like ORFs led to resistance to cyanophages A-1(L) and A-4(L) and to a Fox- phenotype. Electrophoretic analysis showed that interruption of the rfbZ- and rfbP-like ORFs resulted in a change in or loss of the characteristic pattern of the lengths of the LPS, whereas interruption of the rfbD-like ORF merely changed the distribution of the lengths of the LPS to one with a greater prevalence of low molecular weights. According to electron microscopy, interruption of the rfbP-like ORF may have led to aberrant deposition of the layers of the heterocyst envelope, resulting in increased leakage of oxygen into the heterocyst. The results suggest that modified LPS may prevent cyanophage infection of Anabaena sp. vegetative cells and the formation of a functional heterocyst envelope.

Aerobiosis↗

[Cloning of Xanthomonas campestris pv. campestris pathogenicity-related gene sequences by TAIL-PCR].

Southern blot analysis with probe from mini-Tn5 gfp-km transposon indicated that 5 non-pathogenic mutants which were generated by insertion of mini-Tn5 gfp-km mutagenesis contained a single copy of the transposon. Using genomic DNA of each mutant as a template, TAIL-PCR was performed with seven arbitrary degenerate (AD) primers pairing with 3 nested specific primers designed based on the sequence of GFP toward outside in mini-Tn5 gfp-km. After 3-step PCR reactions, the flanking sequence of each mutant was obtained. The PCR product was ligated with pGEM-T EASY vector and then was transformed into E. coli DH5 alpha by electroporation. Positive clones were selected by white/blue colony and plasmid was isolated, then digested with EcoRI. Plasmid was sequenced if its insert was longer than 300 bp. Our results indicated that TAIL-PCR was proved to be a simple and efficient approach in identification of gene using insertion mutagenesis.

Base Sequence↗

Structure and evolution of goat gamma-, beta C- and beta A-globin genes: three developmentally regulated genes contain inserted elements.

We have determined the complete nucleotide sequence of the goat fetal (gamma), preadult (beta C) and adult (beta A) globin genes. In contrast to other globin genes expressed in different stages of development, these three genes are highly homologous (approximately 90%) in both their coding and noncoding regions. The only major difference between them results from elements inserted into their large introns: gamma contains a 247 bp insertion, beta A contains a 318 bp insertion, and beta C contains both a 252 bp insertion and a 60 bp deletion. Based on comparisons of these three genes to each other and to two goat globin pseudogenes, psi beta X and psi beta Z, we conclude that gamma, beta A and beta C have diverged relatively recently, and that the two gene pairs psi beta X - beta C and psi beta Z-beta A arose via a block duplication of an ancestral pseudogene-functional gene pair. Moreover, as opposed to the human fetal genes (G gamma and A gamma), the goat gamma gene appears to be a true beta-like gene that has fetal-specific function. The insertions in gamma, beta A and beta C contain sequence features characteristic of transposon-like elements, and appear to be represented in multiple copies throughout the genome.

Animals↗

Evidence for lateral transfer to Brucellae: characterization of a locus with a Tn-like element (Tn2020).

A genomic locus was discovered within Brucella abortus that contains a novel transposon-like element designated Tn2020. Tn2020 is bounded by a copy of an insertion sequence designated IS2020 and a truncated imperfect copy of IS2020 (tIS2020A). The truncated copy is immediately adjacent to a second copy of IS2020. These data are consistent with the locus having evolved by a complex rearrangement following the transposition of a second copy of Tn2020. Analysis of the organization, orientation, and open reading frames (ORFs) of IS2020 places it within the IS6 family. Four ORFs from Tn2020 were translated in vitro producing a potential transposase with an apparent molecular mass of 27.5 kDa, and three polypeptides with apparent molecular masses of 71 kDa, 22 kDa, and 14 kDa. The central region of Tn2020 encodes the 71 kDa and 14 kDa proteins, while the 22 kDa protein is likely an internal translation initiation product of the IS2020 transposase. The 71 kDa protein shares sequence similarity with several bacterial transcriptional regulatory proteins and may form a helix-turn-helix structure capable of binding DNA. No homologous protein sequences to the 14 kDa peptide were detected in available databases. The 27.5 kDa transposase and its 22 kDa internal translation product shared significant similarity to several transposases from diverse bacterial hosts. Immediately 5' of Tn2020 are genes encoding ribosomal proteins RplU and RpmA. This region also contains a 90 bp sequence that shares significant homology to a repetitive element with inverted repeats from the Sinorhizobium genome. Downstream from Tn2020 is an ORF encoding a protein having significant similarity to a hypothetical protein from Caulobacter. The locus is lower in G+C content from that of the genome. These data suggest that lateral transfer of genetic material has occurred.

Amino Acid Sequence↗