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Infection and Immunity, February 2007, p. 677-683, Vol. 75, No. 2
0019-9567/07/$08.00+0 doi:10.1128/IAI.01067-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
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Laboratoire des Spirochètes, Institut Pasteur,1 Génoscope and CNRS-UMR8030, Atelier de Génomique Comparative,2 Plate-forme Intégration et Analyse Génomique, Institut Pasteur, Paris, France3
Received 7 July 2006/ Returned for modification 16 August 2006/ Accepted 13 November 2006
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Leptospirosis is a worldwide-distributed zoonosis, which is endemic in tropical areas. With the occurrence of large outbreaks in the last decade in areas including Nicaragua (23), Brazil (12), and India (26), leptospirosis is now recognized as an important emerging infectious disease. In industrialized countries, the chance of contracting leptospirosis can increase depending on recreational or occupational exposure. It is estimated that more than 500,000 cases of severe leptospirosis occur annually in the world, with a mortality rate of up to 23% (25). Transmission to humans occurs through direct or indirect contact with urine of infected animals, such as small rodents (15).
Leptospira interrogans is the most frequently reported agent of leptospirosis, with L. interrogans serogroup Icterohaemorrhagiae representing more than half of the leptospires encountered in human infections. Recently, the completion of the genome sequences of L. interrogans serovar Lai and L. interrogans serovar Copenhageni, both belonging to serogroup Icterohaemorrhagiae, was achieved (16, 20). The Lai and Copenhageni sequenced strains were isolated from patients with severe leptospirosis in China (20) and Brazil (16), respectively. It should be noted that while the regular reservoir host for serovar Lai is the striped field mouse (Apodemus agrarius), the host for serovar Copenhageni is the domestic rat (Rattus norvegicus) (15). The L. interrogans genome consists of a 4.33-Mb large circular chromosome and a 350-kb small chromosome (16, 20). The majority of predicted coding sequences (CDSs) of the L. interrogans genome fail to exhibit similarities to proteins of known function in other organisms. The genome is highly conserved between the serovars Lai and Copenhageni, exhibiting 95% identity at the nucleotide level (16). Comparative genomics of these two L. interrogans serovars reveals few genetic differences, including a 54-kb insertion specific to serovar Lai, not found in serovar Copenhageni (Fig. 1). In this study, we show that this 54-kb DNA fragment can both excise from the Lai chromosome and form a circular plasmid.
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FIG. 1. Genomic island of L. interrogans serovar Lai in comparison with the corresponding region in L. interrogans serovar Copenhageni. (A) A chromosomal segment, extending between bp positions 1755000 and 1825000, is represented on this graphical map of the MaGe interface (24). Annotated CDSs are represented in the six reading frames of the sequence by red rectangles, and coding prediction curves are superimposed on the predicted CDSs (blue curves). The synteny maps, calculated on a set of selected genomes, are displayed below. A line contains the similarity results between L. interrogans serovar Lai and one given genome. A rectangle represents a putative ortholog between one CDS of the compared genome and one CDS of the L. interrogans serovar Lai genome. If, for several colocalized CDSs on the L. interrogans serovar Lai genome, there are several colocalized orthologs in the compared genome, the rectangles are all of the same color; otherwise, the rectangle is white. A group of rectangles of the same color thus indicates synteny between L. interrogans serovar Lai and the compared genome. L. interrogans serovar Copenhageni LIC12047 and LIC12044 proteins are similar to LA1765 (the LA1766 protein is a duplication of a 3' region of the LA1765 protein) and LA1848 proteins, respectively, in L. interrogans serovar Lai. Homologs of the two IS1500 open reading frames have been found in synteny with Shewanella oneidensis (second line of the synteny map). The third line shows Bacillus halodurans synteny results in which similar integrases are found but not colocalized (white rectangles). (B) A line plot has been obtained comparing synteny results between L. interrogans serovar Lai and L. interrogans serovar Copenhageni. Putative orthologous relations between the two genomes are defined as gene couples satisfying the bidirectional best hit criterion or a BLASTP alignment threshold, a minimum of 35% sequence identity on 80% of the length of the smallest protein. These relations are subsequently used to search for conserved gene clusters, e.g., synteny groups (syntons). All possible kinds of chromosomal rearrangements are allowed (inversion, insertion, and deletion). A gap parameter, representing the maximum number of consecutive genes which are not involved in a synteny group, is set to five genes. Green, synteny groups are organized on the same strand; red, synteny groups are organized on two opposite strands. chr., chromosome.
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DNA manipulations.
Genomic DNA of Leptospira was isolated using the phenol-chloroform method as previously described (17). For pulsed-field gel electrophoresis (PFGE), cells were embedded in agarose plugs as previously described (5). For digestion, DNA plugs were washed in Tris-EDTA buffer, followed by equilibration in 1x restriction enzyme buffer, and then incubated overnight at 37°C in fresh 1x restriction enzyme buffer containing 30 U NotI restriction enzyme. PFGE was performed in a contour-clamped homogeneous electric field DRII apparatus (Bio-Rad Laboratories, Richmond, CA). Programs with a ramping from 5 to 100 s for 40 h at 170 V or from 10 to 100 s for 40 h at 150 V were used for the resolution of DNA fragments. The DNA was amplified using Taq polymerase (Amersham Biosciences, Little Chalfont, England) under the following conditions: 2 min at 95°C, followed by 35 cycles of 10 s at 95°C, 15 s at 55°C, and 5 min at 72°C, and then one cycle of 10 min at 72°C. For Southern blot analysis, genomic DNA was digested, subjected to electrophoresis in a 1% agarose gel, and transferred onto nylon membranes as previously described (17). Probes were generated by PCR and radiolabeled with [
-32P]dATP using a commercial kit (Megaprime; Amersham Biosciences). Membranes were hybridized overnight at 55 or 60°C in rapid hybridization buffer (Amersham Biosciences) and then washed as previously described (17).
The oligonucleotides listed in Table 1 were used to amplify DNA fragments from L. interrogans serovar Lai.
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TABLE 1. Oligonucleotide primers used in this study
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Sequence analysis. The nucleotide sequences of the genomes of L. interrogans serovar Lai strain Lai 56601 (20) and L. interrogans serovar Copenhageni strain Fiocruz L1-130 (16) were analyzed using MaGe software (http://www.genoscope.cns.fr/agc/mage/) (24). PCR products were sequenced at Genome Express (Meylan, France).
Nucleotide sequence accession numbers. The accession numbers of the nucleotide sequences of the serovar Lai genomic island are EF088430 (5' flanking sequence of the chromosomal locus), DQ890383 (chromosomal empty locus), and DQ890384 and EF100899 (circular intermediates).
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This island is not associated with tRNA genes but is flanked by a putative rhs (rearrangement hot spot)-like gene and an insertion sequence (LA1848 and LA1849) belonging to the IS4 family (Fig. 1 and 2). Rhs elements belong to a set of composite elements found in the chromosome of Escherichia coli. These genes, the function of which remains unknown in E. coli, are typically long CDSs with repetitions and can be found in association with insertion sequences (10). The reason for the association between LaiGI I and the rhs-like gene is not clear.
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FIG. 2. Organization of the genes located in the genomic island locus of L. interrogans serovar Lai. Comparison of the overall organization of the genomic island of L. interrogans serovar Lai (including the published genome sequence and the amplified products that were sequenced) with that of the corresponding region in L. interrogans serovar Copenhageni. Empty boxes indicate the 812- and 170-bp direct repeats at the boundaries of the 54-kb DNA fragment. DNA fragments belonging to LaiGI I are shadowed in gray. CDSs with the same motif are homologs. The locations of primers (Table 1) used for PCR amplification are indicated. The figure is drawn to scale.
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FIG. 3. PCR results showing DNA excision and integration of the 54-kb DNA fragment. PCR amplification for detection of the left end of LaiGI I into the chromosome (P1-P2), the right end of LaiGI I into the chromosome (P3-P4), the circular intermediate with junction of left and right ends of the chromosomal LaiGI I region (P2-P3), and the excision event (P1-P4) in L. interrogans serovar Lai.
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Genomic islands can excise from the chromosome and form circular intermediates (6). Interestingly, genes encoding proteins that could be involved in plasmid segregation were identified in LaiGI I. The segregation of low-copy-number plasmids in bacterial cells is an efficient process that ensures that every daughter cell receives a copy of plasmid DNA, thereby enhancing their inheritance and stability (9). LaiGI I contains putative addiction (LA1780-LA1781) and partition (LA1837-LA1838) modules (see the supplemental material). Addiction modules contain two small genes encoding a potent cell toxin and an antidote protein. In the presence of the addiction module-containing plasmid, the toxicity is neutralized by the antidote protein, which is labile. In contrast, upon loss of the plasmid, the residual stable toxin will likely kill plasmid-free cells. Other toxin-antitoxin loci were identified in the L. interrogans genome (18, 27). Partition modules usually consist of the parA and parB genes, whose products act in conjunction with a centromere-like locus to facilitate faithful plasmid segregation (9). The identification of homologs of partitioning and postsegregational killing genes indicates that LaiGI I could be highly stable in L. interrogans serovar Lai.
The origins of replication of low-copy-number plasmids are often found in the vicinity of parAB. For instance, the rep gene of the leptophage LE1 was found immediately downstream of parAB (2). In LaiGI I, the gene found downstream of the parAB genes, LA1839, encodes a putative protein (381 amino acids in length) unrelated to any other eukaryotic or prokaryotic protein. However, the C-terminal region of the LA1839 protein (from amino acids 153 to 358) shows 50% similarity to the LB376 and LIC20276 proteins, which are encoded by genes located in the putative replication origin of the small chromosome (CII) of L. interrogans serovar Lai and L. interrogans serovar Copenhageni, respectively (16, 20). A 1.5-kb fragment encompassing the LA1839 protein was amplified and then cloned into an E. coli plasmid to generate pORLS. After electroporation with pORLS, we observed plasmid autonomous replication in our laboratory strain Leptospira biflexa and in the pathogen L. interrogans serovar Canicola strain Hond Utrech but not in L. interrogans serovar Lai and L. interrogans serovar Copenhageni (data not shown). However, transformation efficiency was very low (10 transformants per µg of DNA). The absence of transformants in serovars Lai and Copenhageni can therefore be due to poor transformation of the strains and not the absence of plasmid replication. The maintenance of pORLS in leptospiral cell strains suggests that LA1839 is the rep gene of LaiGI I. Consistent with the replication initiation protein (Rep protein), LA1839 encodes a protein containing a predicted helix-turn-helix motif at its N-terminal end that could be involved in DNA binding activity. Finally, the origin of replication of LaiGI I coincides with the polarity switch of the GC skew of the circular plasmid (see the supplemental material). The L. biflexa-E. coli shuttle vector derived from LE1 has already proved to be useful in studies of gene function in saprophytes (2). Our results enable the construction of a new shuttle vector for the genetics of Leptospira, including pathogenic species.
Identification of both a circular intermediate of the genomic island and an empty chromosomal site in L. interrogans serovar Lai.
PFGE analysis of chromosomal DNA after digestion with the rare-cutting restriction enzyme NotI revealed the presence of an additional fragment, larger than 50 kb in size, in comparison to predictions made from the whole-genome sequence of L. interrogans serovar Lai (Fig. 4). Southern hybridization of the blot with specific probes of LaiGI I gave a strong signal with this
50-kb fragment. While DNA probes B and C are physically separated by a NotI restriction site when LaiGI I is inserted into the chromosome, our data indicate that these DNA probes are linked in the
50-kb NotI-digested DNA fragment (Fig. 4). Since LaiGI I contains a single NotI restriction site, this restriction profile is consistent with the linearized form of a circular plasmid corresponding to LaiGI I. No linear replicon was detected by PFGE of undigested DNA and Southern blot hybridization (Fig. 4). Comparison of the in silico restriction map of L. interrogans serovar Lai (20) and PFGE-separated, NotI-digested chromosomal DNA fragments also reveals that a 22-kb fragment predicted by in silico analysis was missing in PFGE. This 22-kb restriction fragment is associated with the chromosomal LaiGI locus (Fig. 4). Consistent with the absence of this segment, the 720-kb NotI-digested DNA deduced from the published sequence should be
688 kb in size (Fig. 4). However, it remains uncertain by PFGE whether the restriction fragment is 688 kb rather than 720 kb (the restriction fragment is located between the 679- and 727-kb fragments of the molecular size standard) (Fig. 4). Evaluation of the ethidium bromide staining intensities of the chromosomal restriction fragment less than 100 kb in length (Fig. 4) also suggests that the majority of LaiGI I DNA remains as a low-copy-number circular plasmid (similar to the chromosome copy number) rather than an integrated form in L. interrogans serovar Lai.
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FIG. 4. Detection of the circular intermediate of LaiGI I by PFGE. (A) Whole genomic analysis of L. interrogans serovar Lai DNA by PFGE. ND, undigested DNA; NotI, digestion with NotI. The arrowhead indicates the additional restriction fragment when the NotI macrorestriction profile was compared with predictions made from the whole-genome sequence of L. interrogans serovar Lai. Asterisks indicate DNA fragments reported as absent (22-kb fragment) or possibly different in length (720-kb fragment) by PFGE compared with predictions made from the whole-genome sequence of L. interrogans serovar Lai (20). For Southern blot analysis, the genomic DNA of L. interrogans serovar Lai was blotted to a nylon membrane and then hybridized at 60°C with the radiolabeled probe B (corresponding to the rep gene). The size marker, on the left, is the bacteriophage DNA multimer (monomer = 48.5 kb). (B) Schematic representation of the macrorestriction patterns from L. interrogans serovar Lai. For Southern blot analysis, the genomic DNA of L. interrogans serovar Lai was blotted to a nylon membrane and then hybridized at 60°C with radiolabeled probes. Probes A, B, C, and D were generated by PCR of total genomic DNA with primer pairs L9a-L9b, 1809a-1809b, 1839a-1839c, and 1850a-1851b, respectively (Table 1). The probes B and C hybridized to the same fragment (located between the 48- and 97-kb fragments of the molecular size standard), indicating the linkage between these two probes. Similarly, probes A and D hybridized to a single macrorestriction fragment (located between the 679- and 727-kb fragments of the molecular size standard). The 22-kb fragment predicted from the published genome sequence (20) is reported as absent. This suggests that the majority of LaiGI I (black box) is not inserted into the chromosome but as a circular plasmid, which is linearized after NotI restriction. Arrows indicate the NotI restriction sites on the large chromosome of L. interrogans serovar Lai (the sizes of restriction fragments are indicated in kilobases).
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LaiGI I is present in other virulent strains. We were interested in determining whether this genomic island is restricted to L. interrogans serovar Lai or is also found in other pathogenic members of the genus. Hybridization analysis demonstrated that sequences highly related or identical to those of this genomic island exist in other L. interrogans strains, i.e., serovars Australis, Bataviae, Canicola, Hebdomadis, and Pyrogenes (Table 2). Transduction, or bacteriophage-mediated gene transfer, is thought to play an important role in the dissemination of genomic islands in other organisms. However, none of the LaiGI I CDSs were found to be homologs of phage-like structural proteins. In addition, genes of LaiGI I are not clearly clustered in large transcription units of related or interacting proteins as in most phage genomes (see the supplemental material). It is possible that the phage genes that are essential for the viral life cycle are not fully functional, so the phage cannot be propagated. This element may also be transferred, if it can really be transferred, to a new host by another mechanism such as conjugation.
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TABLE 2. Distribution of the L. interrogans serovar Lai genomic islanda
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Only recently, the first evidence of gene transfer was demonstrated in L. interrogans by transposition of Himar1, a transposon of eukaryotic origin (3). The putative integrase (encoded by LA1768) and the replication protein (encoded by LA1839) from LaiGI I can be developed as novel tools for the genetics of Leptospira. A better understanding of the molecular biology of this genomic island not only will allow the development of genetic tools but also may lead to improvements in our understanding of virulence and gene dissemination in Leptospira spp.
We thank L. Frangeul for his help in the drawing of the circular map of LaiGI I and I. Saint Girons for her encouragement.
Published ahead of print on 21 November 2006. ![]()
Supplemental material for this article may be found at http://iai.asm.org/. ![]()
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