A Specific Genomic Location within the icm/dot Pathogenesis Region of Different Legionella Species Encodes Functionally Similar but Nonhomologous Virulence Proteins

Abstract

Legionella pneumophila, the major causative agent of Legionnaires' disease, is a facultative intracellular pathogen that grows within human macrophages and amoebae. Intracellular growth involves the formation of a replicative phagosome that requires the Icm/Dot type IV secretion system. Part of the icm/dot region in L. pneumophila contains the icmTSRQPO genes. The proteins encoded by the icmR and icmQ genes were shown to exhibit a chaperone-substrate relationship. Analysis of this region from other pathogenic Legionella species, i.e., L. micdadei and L. longbeachae, indicated that the overall organization of this region is highly conserved, but it was found to contain a favorable site for gene variation. In the place where the icmR gene was expected to be located, other open reading frames that are nonhomologous to each other or to any entry in the GenBank database were found (migAB in L. micdadei and ligB in L. longbeachae). Examination of these unique genes revealed an outstanding phenomenon; by use of interspecies complementation, the icmR, migB, and ligB gene products were found to be functionally similar. In addition, the function of these proteins was usually dependent on the presence of the corresponding IcmQ proteins. Moreover, each of these proteins (IcmR, LigB, and MigB) was found to interact with the corresponding IcmQ proteins, and the genes encoding these proteins were found to be regulated by CpxR. This study reveals new evidence of gene variation occurring in the same genomic location within the icm/dot locus in various Legionella species. The genes found at this site were shown to be similarly regulated and to encode species-specific, nonhomologous, but functionally similar proteins.

Legionella pneumophila, the major causative agent of Legionnaires' disease, is a facultative intracellular pathogen that multiplies within and kills human macrophages and amoebae (14). Besides L. pneumophila, several other Legionella species have been found to be capable of causing pneumonia. L. pneumophila accounts for the vast majority of cases in most of the world, with L. micdadei ranking second and L. longbeachae ranking third (1, 15).

Twenty-five genes required for intracellular multiplication within human macrophages were identified for L. pneumophila and named the icm/dot genes. They were shown to be organized in two separate regions on the genome: region I contains 7 genes (dotDCB, icmWX, and icmV/dotA), and region II contains 18 genes (icmTSRQPONMLKEGCDJB and icmHF) (21, 28). Eighteen of the 25 icm/dot genes encode proteins that contain significant sequence homology to conjugation-related proteins encoded from IncI plasmid R64 (26). Therefore, the Icm/Dot system is believed to form a type IV secretion apparatus through which proteins are translocated across the macrophage plasma membrane (7, 17, 18). Of the seven proteins that are not homologous to proteins that are involved in conjugation, the IcmR and IcmQ proteins (encoded by adjacent genes located in region IIa) were shown to interact with one another (6, 9), and it was proposed that IcmR functions as a chaperone for IcmQ by preventing its aggregation and regulating its pore-forming activity (9, 10).

The whole Icm/Dot system was also found in the Q fever agent Coxiella burnetii, except for the icmR gene (30, 31). In the place where the icmR gene was expected to be located according to the genomic organization of L. pneumophila, five open reading frames (ORFs) were found in C. burnetii.

We were interested in examining whether the icmR locus in the icm/dot region of L. micdadei and L. longbeachae is different from that in L. pneumophila, as in C. burnetii. Here we present new evidence of functionally similar proteins that share no sequence homology to any other proteins (including themselves) and that are all encoded by genes located in the same position in the icm/dot region and regulated by the same response regulator. A similar example of gene variation has not been described before for any type IV secretion system.

MATERIALS AND METHODS

Bacterial strains, plasmids, and media.

The Legionella species and strains used were as follows: L. pneumophila JR32 (wild-type strain), LELA3463 (icmQ), LELA3473 (icmR) (20), GS3001 (icmS) (23), and OG2002 (cpxR) (12); L. longbeachae serogroup 1 ATCC 33462 and L. longbeachae serogroup 2 ATCC 33484 (both clinical isolates); and MF323, MF385, and MF395 (ATCC 33462 icmS, ligB, and icmQ, respectively). The following Legionella species were all clinical isolates, with the exception of L. gratiana: L. micdadei ATCC 33218 and ATCC 33204, L. birminghamensis ATCC 43702, L. bozemanii ATCC 33217, L. cinicinnatiensis ATCC 43753, L. dumoffii ATCC 33343 and ATCC 35850, L. feeleii ATCC 35849, L. gormanii ATCC 43769, L. gratiana ATCC 48413, L. hackeliae ATCC 35250, L. oakridgensis ATCC 700515, L. pneumophila serogroup 3 ATCC 33155, L. sainthelensi ATCC 49322, and L. tucsonensis ATCC 49180. The Escherichia coli strains used were IO7012D (4) and MC1022 (5). Bacterial media, plates, and antibiotic concentrations were used as previously described (23). The plasmids used in this study are listed in Table 1.

TABLE 1.

Plasmids used in this study

Plasmid name	Descriptiona	Reference or source
pBluescript SK(+)	oriR (ColE1) MCS oriR (M13) Apr	27
pGS-lac-02	pAB-1 with promoterless lacZ	13
pLAW344	sacB MCS oriT (RK2) CmrloxP oriR (ColE1) AprloxP	29
pMMB207αB-Km14	RSF1010 derivative; IncQ lacIq Cmr PtacoriT MCS containing α complementation with mobA::Km	24
pT18	oriR (ColEI) T18 fragment of CyaA (amino acids 225-339) Apr	16
pT25	oriR (p15A) T25 fragment of CyaA (amino acids 1-224) Cmr	16
pGS-Lc-35-14	icmQLp gene in pMMB207αB-Km14	31
pGS-Lc-36-14	icmR gene in pMMB207αB-Km14	24
pGS-Lc-37-14	L. pneumophila icmTS genes in pMMB207αB-Km14	24
pKP-T18R	icmR gene in pT18	This study
pKP-T25R	icmR gene in pT25	This study
pKP-T18Q	icmQLp gene in pT18	This study
pKP-T25Q	icmQLp gene in pT25	This study
pMF-SK-long110	pBluescript SK(+) containing L. longbeachae icmT to icmQLl	This study
pMF-long110	L. longbeachae icmT to icmQLl in pMMB207αB-Km14	This study
pMF-long111	ligB gene in pMMB207αB-Km14	This study
pMF-long113	ligB and icmQLl genes in pMMB207αB-Km14	This study
pMF-long114	icmQLl gene in pMMB207αB-Km14	This study
pMF-ligB-lacZ	ligB regulatory region in pGS-lac-02	This study
pMF-ligB::Km	pMF-SK-long110 containing the Kmr cassette inside ligB	This study
pMF-longQ::Km	pMF-SK-long110 containing the Kmr cassette inside icmQLl	This study
pMF-longS::Km	pMF-SK-long110 containing the Kmr cassette inside L. longbeachae icmS	This study
pMF-ligB::Km-GR	pLAW344 containing the insert of pMF-ligB::Km	This study
pMF-longQ::Km-GR	pLAW344 containing the insert of pMF-longQ::Km	This study
pMF-longS::Km-GR	pLAW344 containing the insert of pMF-longS::Km	This study
pMF-T18-ligB	ligB gene in pT18	This study
pMF-T25-ligB	ligB gene in pT25	This study
pMF-T18-longQ	icmQLl gene in pT18	This study
pMF-T25-longQ	icmQLl gene in pT25	This study
pMF-mic47	pBluescript SK(+) containing L. micdadei icmT to icmP	This study
pMF-mic10	L. micdadei icmT to icmQLm in pMMB207αB-Km14	This study
pMF-mic18	icmQLm gene in pMMB207αB-Km14	This study
pMF-mic19	migB gene in pMMB207αB-Km14	This study
pMF-mic21	migB and icmQLm genes in pMMB207αB-Km14	This study
pMF-T18-migA	migA gene in pT18	This study
pMF-T25-migA	migA gene in pT25	This study
pMF-T18-migB	migB gene in pT18	This study
pMF-T25-migB	migB gene in pT25	This study
pMF-T18-micQ	icmQLm gene in pT18	This study
pMF-T25-micQ	icmQLm gene in pT25	This study

^aMCS, multiple cloning site.

Cloning of region IIa from L. longbeachae and L. micdadei.

To clone the icmTSRQPO region from L. longbeachae and L. micdadei, a fragment containing part of their icmP and icmO genes was amplified by PCR with degenerate primers. The resulting fragment was used as a probe for Southern hybridization (22) with L. longbeachae or L. micdadei genomic DNA, and the desired fragment was cloned into pBluescript SK(+) (27). Clones harboring a 4-kb EcoRI-XhoI fragment containing the L. longbeachae icmTS, ligB, and icmQ genes (GenBank accession number AY512558) and a 3.5-kb XhoI-BglII fragment containing the L. micdadei icmTS, migAB, and icmQ genes (GenBank accession number AY512559) were named pMF-SK-long110 and pMF-mic47, respectively. These plasmids were sequenced and used for further analysis.

Plasmid construction for complementation with L. longbeachae genes.

A 4-kb EcoRI-XhoI fragment from pMF-SK-long110 was filled in and cloned into pMMB207αB-Km14 (24) that had been partially digested with SmaI to generate pMF-long110 (containing the icmTS, ligB, and icmQ genes). pMF-long111 (containing the ligB gene) was generated by cloning a 1-kb XmnI-HincII fragment from pMF-SK-long110 into the SmaI site. pMF-long113 (containing the ligB and icmQ genes) was generated by cloning a 2-kb XhoI-NruI fragment from pMF-SK-long110 (that was filled in) into the SmaI site. pMF-long114 (containing the icmQ gene) was generated by cloning a 1.5-kb BalI fragment from pMF-SK-long110 into the same SmaI site.

Plasmid construction for complementation with L. micdadei genes.

A 3.1-kb SmaI fragment from pMF-mic47 was cloned into the SmaI site of pMMB207αB-Km14 to generate pMF-mic10 (containing the icmTS, migAB, and icmQ genes). pMF-mic18 (containing the icmQ gene) was generated by cloning a 1.5-kb SnaI-SmaI fragment from pMF-mic47 into the same SmaI site. pMF-mic19 (containing the migB gene) was generated by cloning a 1-kb BalI-SspI fragment from pMF-mic47 into the SmaI site. To generate pMF-mic21 (containing the migB and icmQ genes), a 1.5-kb BalI-SwaI fragment from pMF-mic47 was cloned into the same SmaI site.

Plasmid construction for allelic exchange.

In order to generate insertions in the L. longbeachae chromosome, a kanamycin resistance cassette digested with PstI was cloned into pMF-SK-long110 that had been partially digested with PstI to generate an insertion in the ligB gene. A kanamycin resistance cassette that had been digested with EcoRV was cloned into pMF-SK-long110 that had been digested with NruI to generate an insertion in the icmS gene or with SwaI to generate an insertion in the icmQ gene. The three resulting plasmids were digested with PvuII, and the inserts were cloned into pLAW344 (29) that had been digested with EcoRV to generate pMF-ligB::Km-GR, pMF-longS::Km-GR, and pMF-longQ::Km-GR. The allelic exchange procedure was performed as previously described (25).

Plasmid construction for the two-hybrid analysis.

To clone the L. pneumophila icmR and icmQ genes, the L. longbeachae ligB and icmQ genes, and the L. micdadei migA, migB, and icmQ genes into the pT18 and pT25 vectors of the Bordetella pertussis cyaA two-hybrid system (16), all of these genes were amplified by PCR with primers designed to form in-frame fusions with the cyaA gene product. Each of the seven genes was amplified with two sets of primers: one PCR product was cloned into pT18 to generate pKP-pT18R, pKP-pT18Q, pMF-T18-ligB, pMF-T18-longQ, pMF-T18-migA, pMF-T18-migB, and pMF-T18-micQ, and the second PCR product was cloned into pT25 to generate pKP-pT25R, pKP-pT25Q, pMF-T25-ligB, pMF-T25-longQ, pMF-T25-migA, pMF-T25-migB, and pMF-T25-micQ. All of these plasmids were sequenced and then introduced as pairs into E. coli IO7012D (ΔcyaA), and lacZ expression levels were measured by using the β-galactosidase assay as previously described (31).

Construction of a lacZ translational fusion.

To generate a ligB::lacZ translational fusion, the regulatory region of the ligB gene was amplified by PCR, digested with BamHI-EcoRI, cloned into pGS-lac-02 (13), and sequenced. Expression levels were measured by using the β-galactosidase assay as previously described (13).

Intracellular growth in Acanthamoeba castellanii and HL-60-derived human macrophages.

Intracellular assays for the growth of L. pneumophila, L. longbeachae, and their derived strains in A. castellanii and HL-60-derived human macrophages were performed as previously described (25).

Low-stringency Southern hybridization.

The Southern hybridization procedure was performed as described previously (22) with 20% formamide.

RESULTS

Region IIa differs among Legionella species.

When region IIa of L. pneumophila was compared with that of C. burnetii in the place where the icmR gene is located in L. pneumophila, five ORFs were found in C. burnetii (an icmR homologue is not present in the C. burnetii genome); four of these ORFs had no homology to any entry in the GenBank database, and the fifth ORF was homologous to a transposase gene. Cloning and sequencing of region IIa from L. micdadei and L. longbeachae (see Materials and Methods) revealed that in the place where the icmR gene was expected to be located (between icmS and icmQ), new ORFs were found; in L. micdadei, two new ORFs were found and named migA and migB (L. micdadei icm gene) (Fig. 1), and in L. longbeachae, one ORF was found in the same location and named ligB (L. longbeachae icm gene) (the ligA gene that was previously described for L. pneumophila [11] is not related to the ligB gene) (Fig. 1). These three genes (migA, migB, and ligB) showed no homology to any entry in the GenBank database, while the icmT, icmS, icmQ, and icmP gene products from the three Legionella species showed a very high degree of homology to one another (the identity between the IcmTSP homologous proteins was 74 to 92%, and that between the IcmQ homologous proteins was 57 to 68%).

FIG. 1.

Schematic drawing of region IIa in C. burnetii, L. pneumophila, L. micdadei, and L. longbeachae. Homologous genes are indicated by different colors or patterns, and the gene names are indicated above the arrows. C. burnetii icmQ contains an N-terminal region that is not present in the other icmQ homologues. The map is not drawn to scale.

For the sake of convenience, the different icmQ genes were named icmQ_Lp, for the L. pneumophila icmQ gene, icmQ_Ll, for the L. longbeachae icmQ gene, and icmQ_Lm, for the L. micdadei icmQ gene.

Distributions of newly discovered genes among different Legionella species.

As shown in Fig. 1, the icmR, ligB, migA, and migB genes were located in the same position (between the icmS and icmQ genes), sharing no sequence homology to one another or to any entry in GenBank, implying that these genes are species specific. In order to verify this hypothesis, we performed low-stringency Southern hybridization with genomic DNA from 18 different Legionella species and strains (described in Materials and Methods) and six different probes—for the L. pneumophila icmS, icmR and icmQ_Lp genes, for the L. longbeachae ligB gene, and for the L. micdadei migA and migB genes. The icmS gene was found in all species examined (Fig. 2A); the same result was obtained for the icmQ_Lp gene (data not shown), indicating the presence of the icm/dot system in all of the species examined. The migB gene was found to be present only in the two L. micdadei strains examined (Fig. 2B), as was the migA gene (data not shown). The icmR gene was found to be present only in the two L. pneumophila strains examined (Fig. 2C). These results indicate that the migA, migB, and icmR genes are indeed species-specific genes (at least in the species examined). Surprisingly, the ligB gene was found in three additional Legionella species besides the two L. longbeachae strains examined (Fig. 2D). This gene was found in L. cincinnatiensis, L. sainthelensi, and L. gratiana, all of which are very closely related to one another (19); these results indicate that the ligB gene is not a species-specific gene. This information suggests that the icmR, ligB, and migAB genes entered the Legionella evolutionary tree through separate branches, while the icmS and icmQ genes entered earlier, as they are also present in C. burnetii. Since seven of the species examined did not contain any of the genes described above, it is possible that each of them has a distinctive gene located in the same position.

FIG. 2.

Analysis of the distributions of icm genes in different Legionella species. The icmS gene is present in all Legionella species examined (A), migB is present in only two L. micdadei strains (B), icmR is present in only two L. pneumophila strains (C), and ligB is present in two L. longbeachae strains and in three additional closely related species (D). Hybridization was performed with chromosomal DNA digested with EcoRI as described in Materials and Methods.

Interspecies complementation.

Due to the high degree of homology among the majority of genes in region IIa (see above), we tested whether the L. longbeachae and L. micdadei region IIa gene products function in a manner similar to that of the L. pneumophila region IIa gene products. Therefore, we performed interspecies complementation assays with L. pneumophila icmS, icmR and icmQ_Lp mutants and complemented each of them with plasmids containing the L. longbeachae and L. micdadei region IIa genes. As expected, full complementation of the L. pneumophila icmS and icmQ_Lp mutants by the L. longbeachae and L. micdadei genes was observed in HL-60-derived macrophages as well as in A. castellanii (data not shown). However, to our surprise, complementation was also obtained for the L. pneumophila icmR mutant, although no icmR homologues were present on either of the complementing plasmids (data not shown). This unexpected result was studied further in order to determine which of the L. longbeachae and L. micdadei region IIa genes was responsible for complementation of the icmR mutant.

IcmR, MigB, and LigB are functionally homologous.

The interspecies complementation assays described above marked the L. longbeachae ligB and L. micdadei migB genes as possible candidates for complementation of the icmR mutant due to their genomic location. To examine whether functional homology exists among the icmR, ligB, and migB gene products, we performed interspecies complementation assays with an L. pneumophila icmR insertion mutant and complemented it with plasmids containing the relevant genes from L. micdadei and L. longbeachae. The strain containing the insertion in the L. pneumophila icmR gene was fully complemented by the plasmid containing the icmR gene alone (Fig. 3A). However, the L. longbeachae ligB gene only partially complemented the L. pneumophila icmR insertion mutant, and the L. micdadei migB gene did not complement it at all (Fig. 3A and B, respectively). Nevertheless, plasmids containing a combination of the L. longbeachae ligB and icmQ_Ll genes or the L. micdadei migB and icmQ_Lm genes completely restored the ability of the icmR insertion mutant to grow intracellularly in HL-60-derived macrophages (Fig. 3A and B, respectively), although no icmR homologue was present on these plasmids. Similarly, in A. castellanii, neither the ligB gene nor the migB gene complemented the icmR insertion mutant, but a combination of the L. longbeachae ligB and icmQ_Ll genes or the L. micdadei migB and icmQ_Lm genes fully complemented the same insertion mutant (Fig. 3C and D, respectively). The data presented in Fig. 3 indicate that the ligB, migB, and icmR genes are functionally similar and that the presence of the L. longbeachae LigB and IcmQ_Ll proteins together or the L. micdadei MigB and IcmQ_Lm proteins together may have a significant role in pathogenesis which is similar to the role of the L. pneumophila IcmR and IcmQ_Lp proteins. These results clearly indicate that although no sequence homology exists among the icmR, migB, and ligB genes, they seem to function similarly and their participation in the virulence pathway is related to the corresponding icmQ genes.

FIG. 3.

Interspecies complementation of the L. pneumophila icmR insertion mutant. Experiments were performed with HL-60-derived human macrophages (A and B) or A. castellanii (C and D). Symbols: ⧫, wild-type L. pneumophila JR32; ▪, L. pneumophila icmR mutant (LELA3473) containing the vector; ✻, L. pneumophila icmR gene; ▵, L. longbeachae ligB gene; ▴, L. longbeachae ligB and icmQ_Ll genes; ○, L. micdadei migB gene; •, L. micdadei migB and icmQ_Lm genes. The experiments were performed at least three times, and similar results were obtained. The error bars indicate standard deviations.

Analysis of IcmQ proteins from three Legionella species.

The finding that L. longbeachae region IIa and L. micdadei region IIa complemented the icmQ_Lp insertion mutant predicted that the icmQ_Ll and icmQ_Lm genes, respectively, were responsible for these results. However, the complementation results for the L. pneumophila icmR mutant predicted that the IcmQ_Ll and IcmQ_Lm proteins function together with the protein encoded by the gene located upstream from their genes. These two observations led us to examine whether the icmQ_Ll and icmQ_Lm genes by themselves can complement the icmQ_Lp mutant. When examined in A. castellanii, the icmQ_Ll gene only partially complemented the icmQ_Lp mutant (Fig. 4C), while the icmQ_Lm gene did not complement it at all (Fig. 4D). However, plasmids containing a combination of the L. longbeachae ligB and icmQ_Ll genes or the L. micdadei migB and icmQ_Lm genes together fully complemented the icmQ_Lp insertion mutant in A. castellanii (Fig. 4C and D, respectively). When examined in HL-60-derived macrophages, the icmQ_Ll gene fully complemented the ability of the icmQ_Lp mutant to grow intracellularly, whereas the icmQ_Lm gene only partially complemented this mutant (Fig. 4A and B, respectively). In this situation, too, a plasmid containing the L. micdadei migB and icmQ_Lm genes was found to fully complement the icmQ_Lp insertion mutant in HL-60-derived macrophages (Fig. 4B), implying that a combination of the L. micdadei migB and icmQ_Lm genes was required for the complementation to occur. These results indicate that the icmQ_Ll and icmQ_Lm genes require the presence of the relevant gene located upstream from them for complete complementation, even though they are both homologous to the icmQ_Lp gene.

FIG. 4.

Interspecies complementation of the icmQ_Lp insertion mutant. The experiments were performed with HL-60-derived human macrophages (A and B) or A. castellanii (C and D). Symbols: ⧫, wild-type L. pneumophila JR32; ▪, icmQ_Lp mutant (LELA3463) containing the vector; ✻, icmQ_Lp gene; ○, icmQ_Ll gene; •, L. longbeachae ligB and icmQ_Ll genes; ▵, icmQ_Lm gene; ▴, L. micdadei migB and icmQ_Lm genes. The experiments were performed at least three times, and similar results were obtained. The error bars indicate standard deviations.

The L. longbeachae icm genes are required for intracellular growth.

Since the involvement of the icm genes in L. longbeachae pathogenesis has not been examined before, three insertion mutations in the L. longbeachae icmS, ligB, and icmQ_Ll genes were constructed. All of the intracellular growth experiments with L. longbeachae strains were performed with HL-60-derived human macrophages, since L. longbeachae does not grow in A. castellanii (data not shown). The L. longbeachae icmS gene was found to be required for intracellular growth, and it was complemented by the L. longbeachae, L. pneumophila, and L. micdadei icmS genes (data not shown). The icmQ_Ll insertion mutant showed a partial intracellular growth defect, which was fully complemented by the icmQ_Lp, icmQ_Ll, and icmQ_Lm genes (Fig. 5A). The ligB insertion mutant also showed a partial intracellular growth phenotype, which was completely restored by complementing plasmids containing the ligB or the icmR gene (Fig. 5B) but not the migB gene or a combination of the migB and icmQ_Lm genes (Fig. 5B). These results show that the L. longbeachae icmS, ligB, and icmQ_Ll genes are required for intracellular growth, that the ligB and icmR genes are functionally similar, but that the migB gene functions in a manner similar to that of the icmR gene (Fig. 2B) but not that of the ligB gene (Fig. 5B).

FIG. 5.

Interspecies complementation of L. longbeachae mutants. (A and B) Complementation analysis of the icmQ_Ll (A) and ligB (B) mutants with HL-60-derived human macrophages. Symbols for panel A: ⧫, wild-type L. longbeachae ATCC 33462; □, icmQ_Ll mutant (MF395) containing the vector; +, icmQ_Ll gene; ▴, icmQ_Lp gene; ○, icmQ_Lm gene. Symbols for panel B: ⧫, wild-type L. longbeachae ATCC 33462; ▪, L. longbeachae ligB mutant (MF385) containing the vector; ▴, L. longbeachae ligB gene; ▵, L. pneumophila icmR gene; ○, L. micdadei migB gene; •, L. micdadei migB and icmQ_Lm genes. The experiments were performed at least three times, and similar results were obtained. The error bars indicate standard deviations.

IcmQ interacts with IcmR, MigB, and LigB.

The functional homology among the three nonhomologous proteins (IcmR, LigB, and MigB), in addition to previous reports showing that the IcmR and IcmQ_Lp proteins interact with one another (6, 9), led us to analyze whether each of the IcmR, MigB, and LigB proteins interacts with the corresponding IcmQ protein. For this analysis, a bacterial two-hybrid system that is based on the CyaA toxin of B. pertussis was used (16). The L. pneumophila icmR and icmQ_Lp genes, the L. longbeachae ligB and icmQ_Ll genes, and the L. micdadei migA, migB, and icmQ_Lm genes were fused to the T18 (N-terminal fusion) and T25 (C-terminal fusion) fragments, and interactions among them were examined. In this system, an interaction between two proteins results in cyclic AMP production, which is determined by measuring the levels of expression of the lacZ gene product.

As shown in Fig. 6A to C, each of the three proteins interacts with the corresponding IcmQ protein (the MigA protein does not interact either with the IcmQ_Lm protein or with the MigB protein) (Fig. 6C), strongly supporting the notion that the IcmR, LigB, and MigB proteins play similar roles and that their functions involve interactions with the corresponding IcmQ protein. Moreover, the interaction between each of the three proteins and the corresponding IcmQ protein was very strong when the IcmQ protein was fused to the T18 fragment and the when the IcmR/LigB/MigB proteins were fused to the T25 fragment, while the interaction in the opposite direction was significantly weaker. These results indicate that the interactions of the proteins examined probably occur between the C-terminal domain of the IcmR/LigB/MigB proteins and the N-terminal domain of the corresponding IcmQ protein.

FIG. 6.

Two-hybrid analysis of the interactions between the L. pneumophila, L. longbeachae, and L. micdadei protein pairs. Interactions were examined for the L. pneumophila IcmR and IcmQ_Lp proteins (A), the L. longbeachae LigB and IcmQ_Ll proteins (B), and the L. micdadei MigB and IcmQ_Lm proteins (C); interspecies interactions were examined for the IcmQ_Lp protein (D), the IcmQ_Ll protein (E), and the IcmQ_Lm protein (F). β-Galactosidase activity was measured in Miller units [M.U.] at stationary phase. The names of the genes used in this assay are marked with a code composed of two letters and a number between them. The letter on the left represents the species: P, L. pneumophila; L, L. longbeachae; M, L. micdadei. The number indicates to which cyaA fragment the examined gene was fused: 18, T18; 25, T25. The letter on the right represents the gene examined: R, icmR; A, migA; B, ligB (when the left letter is L) or migB (when the left letter is M); Q, icmQ. The results are the averages and standard deviations of at least three independent experiments.

In order to reinforce these observations, we performed interspecies interaction assays to examine all of the possible combinations of the IcmR/LigB/MigB proteins and the IcmQ_Lp, IcmQ_Ll, and IcmQ_Lm proteins. Interactions were observed for all of the protein combinations (Fig. 6D to F), with the exception of MigB, which did not interact with either IcmQ_Lp (Fig. 6D) or IcmQ_Ll (Fig. 6E). This finding correlates with our results showing that the migB gene by itself did not complement the icmR or the ligB mutant (Fig. 3B and 5B) and can be explained by the fact that L. micdadei is evolutionarily more distant from L. longbeachae than L. pneumophila (19). All of the interactions observed occurred in the same orientation as that described above (Fig. 6D to F) and were significantly weaker in the opposite orientation (data not shown), indicating that indeed a specific orientation of the IcmR/LigB/MigB proteins is required for their interaction with the corresponding IcmQ protein. Very recently, it was shown that IcmQ_Lp binds to IcmR via its N-terminal domain (10), a finding that strongly supports our results.

icmR, ligB, and migB are regulated by CpxR.

Although no sequence homology exists among icmR, ligB, and migB, the finding that they function similarly led us to wonder whether their expression is regulated in the same manner. It has been shown that the L. pneumophila icmR gene is positively regulated by the CpxRA two-component system through a conserved CpxR binding site (12). Careful examination of the regulatory region of the ligB and migB genes revealed that a putative CpxR binding site is also found in the ligB and migB regulatory regions (Fig. 7A). It also seems, from a comparison of the sequences shown in Fig. 7A, that the Legionella consensus binding site for the CpxR response regulator (GTAAAn₆GAAA) is slightly different from the one identified in E. coli: GTAAAn₅GTAAA (8). In order to test whether these genes are indeed regulated by the same response regulator, we constructed a translational fusion between the L. longbeachae ligB regulatory region and the lacZ reporter gene and introduced the resulting plasmid into L. longbeachae, L. pneumophila, and an L. pneumophila strain containing an insertion mutation in the cpxR gene. β-Galactosidase activity was measured at stationary phase, and the results obtained strongly indicated that the cpxR mutant drastically reduced the level of expression of ligB (Fig. 7B). These results suggest that the icmR/ligB/migB genes are probably regulated similarly, a fact that correlates with the functional homology described above for the three proteins encoded by these genes.

FIG. 7.

The icmR, ligB, and migB genes are probably regulated by CpxR. (A) Part of the regulatory region of the L. pneumophila icmR, L. longbeachae ligB, and L. micdadei migB genes. The consensus recognition sequence of CpxR identified in E. coli is shown at the bottom. CpxR recognition sequences are shown in bold type and are underlined, and the distances to the first ATG are indicated. (B) Expression of a ligB::lacZ translational fusion in L. longbeachae (Ll), L. pneumophila (Lp), and an L. pneumophila cpxR gene insertion mutant (ΔcpxR) at stationary phase. The results, reported in Miller units (M.U.), are the averages and standard deviations of at least three independent experiments.

DISCUSSION

L. pneumophila grows intracellularly and kills the host cell due to the activity of the Icm/Dot type IV secretion system, which is believed to form a protein complex that translocates effector proteins from the bacterial cytoplasm into the host cell. The icm/dot system was recently discovered also in C. burnetii and included all of the icm/dot genes except for icmR (30, 31). The icmR gene, together with icmQ_Lp, is located in region IIa; their gene products are predicted to be found in the bacterial cytoplasm and are not homologous to conjugation-related proteins encoded by plasmid R64. This information, together with the finding that C. burnetii contains the entire icm/dot system except for icmR, led us to focus on region IIa as a potential cause for differences between bacteria that contain the Icm/Dot virulence system.

Besides L. pneumophila, several pathogenic Legionella species have been described, and we chose to study two of them: L. micdadei which is the second most common agent of Legionnaires' disease in the world, and L. longbeachae, which is the third most common etiological agent of Legionnaires' disease in the world but the dominant agent in Australia (1, 15). Cloning and sequencing of region IIa from L. longbeachae and L. micdadei revealed an interesting discovery: the icmR gene was found to be missing in the region between icmS and icmQ in both species, and other ORFs were found in its place. In L. longbeachae, one ORF (ligB) was found in the place where icmR was expected to be located, and in L. micdadei, two ORFs (migA and migB) were found in the same position. In order to investigate the functions of these newly discovered gene products, a homology search was performed, but no homology was detected among the IcmR, LigB, and MigB proteins or to any other entry in GenBank.

These proteins seem to share a few properties in common with type III virulence-related chaperones. (i) The IcmR, MigB, and LigB proteins were all predicted by the PSORT program (http://psort.ims.u-tokyo.ac.jp) to be located in the bacterial cytoplasm. They were also predicted to have acidic pIs (4.75, 5.3, and 5.8, respectively), and they are all small proteins (88 to 120 amino acids). These properties are considered common features of type III secretion chaperones (2). (ii) Through interspecies complementation experiments, the IcmR, LigB, and MigB proteins were found to function similarly, although no sequence homology exists among them. Bioinformatics programs predicted that these three proteins contain an α-helical structure at their C-terminal domain, like that found for type III chaperones, which also do not share any sequence homology but which are structurally homologous (3). (iii) As was shown before for the L. pneumophila IcmR and IcmQ_Lp proteins (6, 9), analysis of protein interactions showed that the L. longbeachae LigB and L. micdadei MigB proteins also interact with their corresponding IcmQ proteins and that the interactions occur via the C-terminal domain of the IcmR, LigB, or MigB protein and the N-terminal domain of the relevant IcmQ protein. It was shown before that type III virulence-related chaperones interact with their substrates in a specific orientation similar to the one described above (2). (iv) Type III chaperones are encoded by genes adjacent to the genes encoding their substrates, like IcmR, LigB, and MigB, which were shown to interact with the protein encoded by the gene located downstream from their genes (IcmQ).

All of the information described above strongly implies that the IcmR, LigB, and MigB proteins function similarly, probably as chaperones of the relevant IcmQ proteins. Even though the IcmR, LigB, and MigB proteins seem to share several properties in common with type III chaperones, other characteristics make these proteins quite distinct. First, all of these features of type III chaperones were found here in a type IV secretion system. Second, in a type III secretion system, each chaperone interacts with a specific substrate and not with similar substrates, as was found here. Another unique feature of these proteins is the specific location of their genes on the chromosomes of different Legionella species, a property that has not been described for type III chaperones.

As mentioned above, the C. burnetii genome contains the entire icm/dot system except for the icmR gene. However, the five ORFs that are located in its place encode large nonacidic proteins; therefore, it is highly unlikely that one of these proteins plays a role similar to that of IcmR, LigB, or MigB. In addition, it was proposed before that the C. burnetii IcmQ protein, which was shown not to complement the icmQ_Lp mutant (30, 31), functions as its own chaperone, as it contains an extension of 47 amino acids at its N-terminal domain (Fig. 1).

Our results reveal new evidence of gene variation at a specific position in the pathogenicity region of different Legionella species; this finding has not been shown before for any type IV secretion system. The genes located at this site encode proteins that share no sequence homology but seem to function similarly and to be controlled by the same regulator. These findings lead to two main questions. (i) What is the mechanism that causes this gene variation? (ii) Why does such gene variation exist? As far as the first question, the evolutionary process that led to this intriguing phenomenon is quite mysterious due to the lack of evidence for horizontal gene transfer; this region does not contain any differences in its GC content, and no insertion sequence elements have been found in this region in the three Legionella species examined. The possible answer to the second question might be related to a recent study showing that IcmQ_Lp functions as a pore-forming protein (10). This information leads to the hypothesis that the IcmQ_Lp, IcmQ_Ll, and IcmQ_Lm proteins may be adapted to insert pores into the membrane of their specific protozoan host, a function that is mediated by the IcmR, LigB, and MigB proteins, respectively. It is possible that these proteins are part of a machinery that evolved to adapt a specific Legionella species to a certain amoeba host, thus functioning as host-specific determinants. These differences in the icm/dot systems of the three Legionella species examined may be directly or indirectly related to the fact that of these three species, L. pneumophila is the most common causative agent of Legionnaires' disease in the world.