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J Bacteriol. Jun 1998; 180(11): 2866–2874.
PMCID: PMC107251

Genes Essential for Nod Factor Production and Nodulation Are Located on a Symbiotic Amplicon (AMPRtrCFN299pc60) in Rhizobium tropici


Amplifiable DNA regions (amplicons) have been identified in the genome of Rhizobium etli. Here we report the isolation and molecular characterization of a symbiotic amplicon of Rhizobium tropici. To search for symbiotic amplicons, a cartridge containing a kanamycin resistance marker that responds to gene dosage and conditional origins of replication and transfer was inserted in the nodulation region of the symbiotic plasmid (pSym) of R. tropici CFN299. Derivatives harboring amplifications were selected by increasing the concentration of kanamycin in the cell culture. The amplified DNA region was mobilized into Escherichia coli and then into Agrobacterium tumefaciens. The 60-kb symbiotic amplicon, which we termed AMPRtrCFN299pc60, contains several nodulation and nitrogen fixation genes and is flanked by a novel insertion sequence ISRtr1. Amplification of AMPRtrCFN299pc60 through homologous recombination between ISRtr1 repeats increased the amount of Nod factors. Strikingly, the conjugal transfer of the amplicon into a plasmidless A. tumefaciens strain confers on the transconjugant the ability to produce R. tropici Nod factors and to nodulate Phaseolus vulgaris, indicating that R. tropici genes essential for the nodulation process are confined to an ampliable DNA region of the pSym.

Bacteria belonging to Rhizobium and related genera are able to establish a symbiosis with leguminous plants which culminates in the formation of nitrogen-fixing nodules. Nodule formation is the result of a cellular differentiation process mediated by molecular signal exchange which involves the expression of specific genes in both partners. In response to plant flavonoid compounds, the bacteria produce a family of lipo-chito-oligosaccharide molecules, called nodulation (Nod) factors, which in turn elicit nodule development on roots or stems of the legumes (5, 30). Rhizobium nodulation (nod, nol, and noe) genes involved in the production of Nod factors are located primarily on large plasmids, called symbiotic plasmids or pSyms (3, 28).

In Rhizobium, both plasmid and chromosome replicons contain a large amount of reiterated DNA sequences (9). These repeated DNA sequences include complete operons, specific genes, regulatory sequences, and insertion sequence (IS) elements (27). The recently reported sequence of the pSym of Rhizobium sp. strain NGR234 revealed that most of the repeated sequences correspond to IS-type elements (11). We have shown that repeated sequences participate in recombination events leading to genomic rearrangements. We have used the term “amplicon” to denote a DNA region, bordered by direct repeated sequences, that has the potential to be amplified. The first Rhizobium amplicon was identified in Rhizobium etli CFN42 and consists of a 120-kb DNA region bordered by nifHDK repeats (25). Subsequently, other amplicons have been identified either on the chromosome or on the pSym or other plasmids of R. etli (10, 26). Amplification may also be induced potentially in any region of the genome by genetic manipulations that generate amplicon-type structures. We have recently applied a random DNA amplification strategy to the pSym of Rhizobium tropici to generate strains with improved symbiotic properties (20).

Natural DNA amplification, generated by repeated sequences present in the genome, occurs at high frequency under laboratory conditions (10, 25, 26). Little, however, is known about its consequences in the Rhizobium-legume symbiosis. In this study, we demonstrate the presence of natural DNA amplification in the symbiotic region of the pSym of R. tropici CFN299. A symbiotic amplicon, which we call AMPRtrCFN299pc60, was isolated and characterized. Since mobilization of this amplicon into Agrobacterium tumefaciens enables the transconjugant to produce R. tropici Nod factors and to form nodules on Phaseolus vulgaris, we conclude that the genes essential for nodulation are confined to an amplicon structure.


Bacterial strains, plasmids, and growth conditions.

The bacterial strains and plasmids used are listed in Table Table1.1. Escherichia coli strains were grown on Luria-Bertani medium (1% peptone, 0.5% yeast extract, 1% NaCl) supplemented with the following antibiotics at the indicated concentrations (micrograms per milliliter): ampicillin, 100; chloramphenicol, 15; gentamicin, 25; kanamycin, 50; nalidixic acid, 20; and tetracycline, 10. Rhizobium and Agrobacterium strains were cultivated at 30°C on PY medium (0.5% peptone, 0.3% yeast extract, 10 mM CaCl2) with the following antibiotics, at the indicated concentrations (micrograms per milliliter), when required: chloramphenicol, 30; kanamycin, 30 to 300; nalidixic acid, 20; neomycin, 60; and rifampin, 100. Triparental matings, using E. coli 1830/pJB3JI as a helper, were performed as described previously (20).

Bacterial strains and plasmids used

DNA manipulations.

Standard techniques such as isolation of genomic DNA, plasmid purification, DNA cloning and restriction, agarose gel electrophoresis, DNA labelling, and filter blot hybridization were performed as described previously (9, 20). Plasmid profiles were obtained by using a modified Eckhardt technique (6) as described by Hynes and McGregor (14). A genomic library of R. tropici CFN299 was made by cloning partially EcoRI-digested total DNA into the cosmid vector pSUP205. DNA amplification was quantified by densitometric integration of the hybridization signals from autoradiographs, using the Eagle Eye II system (Stratagene, La Jolla, Calif.).

Isolation of R. tropici strains carrying an amplification in the pSym.

For this purpose, a 2.2-kb PstI-SalI DNA fragment containing the nodHPQ genes of R. tropici strain CFN299 cloned into pJQ200sk was used. A cartridge constituted by a 6.5-kb BglII-PstI DNA fragment from plasmid pTn5luxB (15a) was ligated into pIC20R and cut out by BglII-BamHI digestion, giving rise to GDYN3. GDYN3 contains a gene encoding kanamycin resistance (Km) from Tn903 as well as conditional origins for conjugal transfer (oriT) and replication (oriV) of the broad-host-range plasmid RK2 (8). GDYN3 (Km-oriVT) was then inserted into the unique BamHI site of the nodP gene. The resulting recombinant plasmid, designated pPAM37, was transformed into E. coli S17-1 and from there transferred into R. tropici wild-type strain CFN299 by biparental mating. Double recombinants of R. tropici carrying GDYN3 in the pSym were selected on PY medium containing nalidixic acid 5% sucrose, and 30 μg of kanamycin per ml. The site of GDYN3 insertion was ascertained by Southern hybridization (see Results). One of these R. tropici exconjugants was named CFNX302. To isolate R. tropici derivatives carrying amplifications, strain CFNX302 was grown at 30°C in PY broth medium to log phase. Serial dilutions were prepared in a solution containing 10 mM MgSO4 and 0.01% (vol/vol) Tween 40. Appropriate dilutions were plated on PY agar plates supplemented with 50, 100, 150, 200, 250, and 300 μg of kanamycin per ml. After incubation at 30°C for 4 days, small and large colonies were obtained. Analysis of plasmid profiles showed that only the larger colonies (which appeared at a frequency of 10−4) exhibited amplification in the pSym (see Results). Two of the clones carrying amplifications were isolated on 150 μg of kanamycin per ml and designated CFNX303 and CFNX304.

Mobilization of Rhizobium symbiotic amplicons into E. coli and A. tumefaciens.

E. coli DH5α and A. tumefaciens GMI9023 containing plasmid pEYM5 were used as recipients. Plasmid pEYM5, which carries a helper function (trfA) of replication at oriV (35a), was introduced into the strains by biparental mating with S17-1/pEYM5 as a donor. Rhizobium amplicons were first mobilized into E. coli DH5α/pEYM5 by using Rhizobium amplified derivatives CFNX303 and CFNX304 as donors in triparental matings. E. coli exconjugants containing Rhizobium amplicons as stable plasmids were selected on LB agar plates supplemented with nalidix acid, chloramphenicol, and kanamycin. The plasmids isolated from 60 E. coli exconjugants, 30 clones per mating, had identical restriction patterns. Two of these E. coli exconjugants, CFNC303 and CFNC304, were used as donors to transfer the Rhizobium amplicon into A. tumefaciens GMI9023/pEYM5 by triparental mating. A. tumefaciens exconjugants bearing Rhizobium amplicons were selected on PY agar plates containing chloramphenicol, neomycin, and rifampin. Two of these A. tumefaciens exconjugants were designated CFNA303 and CFNA304.

Cloning and sequencing of endpoints of the amplicon.

The smaller 2.5-kb EcoRI fragment that borders the amplicon was purified from agarose gels by using a Nucleotrap kit (Macherey-Nagel, Düren, Germany) and cloned into pUC19. The nucleotide sequence of the cloned fragment was determined with a ALF DNA sequencer (Pharmacia Biotech, Uppsala, Sweden). Sequencing reactions were performed with alkaline-denaturated double-stranded DNA as a template. Oligonucleotides were designed to complete the nucleotide sequence determination of both DNA strands. Sequences were analyzed using the GCG (version 8.0.1-UNIX 1994; University of Wisconsin, Madison) and PCGENE (Intelligenetics, Mountain View, Calif.) software packages. Sequence comparisons were done by using the BLAST program (1).

TLC and HPLC analysis of Nod factors.

Nod metabolites for thin-lay chromatography (TLC) and high-pressure liquid chromatography (HPLC) analysis were obtained as described previously (16). Briefly, 1 ml (TLC) or 10 ml (HPLC) of liquid minimal medium (22) was inoculated with fresh overnight cell cultures to an optical density at 600 nm of 0.1. For A. tumefaciens, 0.1% (wt/vol) Casamino Acids was added to the medium (pH 7.0). When required, apigenin (1.2 μmol per liter) was added as a nod gene inducer. Nod metabolites were radiolabeled with 2 μCi of [35S]sulfate or 0.1 μCi of d-[U-14C]glucosamine. After 12 h of growth, Rhizobium or Agrobacterium cell supernatants were passed through a C18 Sep-Pak cartridge (Waters Millipore, Milford, Mass.), and hydrophilic molecules were washed out with 10 ml of autoclaved deionized water. Nod metabolites were then eluted with 3 ml of methanol and dried under N2 at 35°C. For TLC, Nod metabolite fractions were loaded onto reverse-phase TLC plates (RP-18 F254s; Merck, Darmstadt, Germany). Migration was performed with methanol-ammonia (5.5 N; 9:1, vol/vol) as the mobile phase. Radiolabeled compounds were revealed by autoradiography on Hyperfilm-ßmax (Amersham). For HPLC, samples were applied to a reverse-phase C18 cartridge (LiChropher 100 RP-18, 5 μm; Merck), and Nod metabolites were eluted with the gradient described previously (22). The eluate was monitored at 220 nm, and analysis was performed by comparison with elution times of purified sulfated (10 min) and nonsulfated (14 min) Nod factors.

Plant nodulation assays.

Plant nodulation assays were performed as described previously (20). Seeds of P. vulgaris cultivars Negro Jamapa, N-8-116, and BAT-477 were surface disinfected and germinated on water agar plates. Germinated seedlings were transferred to 250-ml Erlenmeyer flasks containing Fahraeus (7) medium with vermiculite; 5 × 105 Rhizobium or Agrobacterium cells were used to inoculate plant roots. The identity of nodule isolates was ascertained by antibiotic resistance and confirmed when necessary by Southern blot hybridization analysis of plasmid profiles.

Light and electron microscopy.

Microscopy of nodules was performed as described previously (36). Nodules were harvested from bean seedlings 21 days after inoculation and fixed in 3% glutaraldehyde in 0.1 M potassium phosphate buffer. Segments were washed in buffer, postfixed for 2 h at 4°C in 1% osmium tetroxide, dehydrated in ethanol, and embedded in Epon resin or in ore. Light microscopy was performed with thick sections (about 1 μm) stained with 0.05% toluidine blue. Scanning microscopy was performed at 15 kV with a JEOL 5410 LB microscope. For electron microscopy, ultrathin sections (about 80 nm) were stained in aqueous 2% uranyl acetate and observed at 60 kV with a JEOL 1200 EX2 electron microscope.

Nucleotide sequence accession number.

The nucleotide sequence of ISRtr1 is under GenBank accession no. AF041379.


Experimental strategy to search for Rhizobium symbiotic amplicons.

The genetic element GDYN3 was constructed (see Materials and Methods), and a recombinant plasmid (pPAM37) containing the nodHPQ genes interrupted in nodP by the GDYN3 element was introduced into R. tropici by conjugation from E. coli. Double recombinants of R. tropici bearing the nodP::GDYN3 allele in the homologous region of the pSym were selected (Fig. (Fig.1A).1A). The site of the insertion of GDYN3 was ascertained by hybridization of Southern blots of total DNA digested with EcoRI from recombinant strains (not shown). Recombination between direct repeats flanking the region containing GDYN3 leads to a tandem duplication of a whole amplicon structure. The tandemly duplicated region may serve as a substrate for recombination, leading to further amplification or deletion (Fig. (Fig.1B).1B). R. tropici derivatives carrying amplifications were selected by increasing the kanamycin concentration in the culture medium. Amplification was ascertained by the analysis of plasmid profiles (see below).

FIG. 1
Experimental approach to identify Rhizobium symbiotic amplicons. (A) Plasmid pPAM37, containing the subcloned nodHPQ genes with the GDYN3 insertion in nodP, was introduced via conjugation into the wild-type R. tropici strain CFN299. When a double-crossover ...

When deletion events occur in amplified regions, closed circular structures containing the whole amplified region in either a monomeric or multimeric form are generated. The presence of oriT and oriV on the excised amplicons provides the possibility for their isolation. To do this, R. tropici amplified derivatives were used as donors using E. coli containing plasmid pEYM5 as the recipient (Fig. (Fig.1C).1C). This IncQ plasmid has a broad host range and harbors the trfA gene, which encodes a transactivator of oriV. Exconjugants of E. coli were selected, and all harbored a plasmid of approximately 66 kb containing Rhizobium sequences (see below). Amplicons were then mobilized from E. coli exconjugants into A. tumefaciens GMI9023 carrying plasmid pEYM5 (Fig. (Fig.1D).1D). A. tumefaciens exconjugants bearing Rhizobium amplicons were selected. The presence of Rhizobium sequences in the A. tumefaciens exconjugants was confirmed (see below).

All steps of the experimental strategy (gene replacement to introduce the GDYN3 element, amplification in Rhizobium, in vivo cloning of the amplicon sequence in E. coli, and its transfer to A. tumefaciens) were monitored by the analysis of plasmid profiles of the different strains involved (Fig. (Fig.2).2). Wild-type R. tropici (CFN299) harbors four plasmids (pa, pb, pc, and pd). Plasmid pc of 490 kb is the pSym. As expected, the pSym pattern of amplified derivatives shows bands of larger size. Hybridization of plasmid profiles with a nodHPQ probe confirmed the presence of monomers, dimers, and trimers of closed circular DNA containing amplicon sequences in amplified derivatives. E. coli (CFNC303 and CFNC304) and A. tumefaciens (CFNA303 and CFNA304) transconjugants contained a plasmid of approximately 66 kb that hybridized with the R. tropici nodHPQ probe.

FIG. 2
Plasmid profiles of R. tropici, A. tumefaciens, and E. coli strains, stained with ethidium bromide (odd-numbered lanes) or hybridized against a nodHPQ probe (even-numbered lanes). Strains used were R. tropici CFN299 (wild type) (lanes 1 and 2), R. tropici ...

Characterization of the R. tropici symbiotic amplicon.

The amplicon identified was named AMPRtrCFN299pc60 (see Discussion). nodHPQ genes and the amplicon DNA sequence, represented by plasmid pCFNC303 (isolated from E. coli CFNC303), were used to hybridize against colonies from a genomic library of total R. tropici DNA made in pSUP205. Several overlapping cosmids were isolated. The relative positions of five overlapping cosmids covering the whole amplicon are shown in Fig. Fig.3a.3a. Localization of the amplicon sequences in the cosmid contig was performed by hybridization of AMPRtrCFN299pc60 against the ordered cosmids digested with EcoRI (not shown). Comparative hybridization analysis of total DNA digested with EcoRI of different strains (the wild-type strain, the derivative containing GDYN3, the amplified strains, as well as E. coli and A. tumefaciens bearing amplicons) against the DNA from AMPRtrCFN299pc60 (not shown) allowed the construction of the physical map of the amplicon (Fig. (Fig.3).3). In the wild-type strain, seven regions were defined (Fig. (Fig.3b).3b). Regions A and Z contain the borders of the amplicon. The inner regions were named B, C, D, E, and F. Regions A, C, D, E, and Z correspond to single EcoRI fragments. Regions B and F contain two and three EcoRI sites, respectively, that were not mapped between them. As expected, in the R. tropici strain containing the GDYN3 element (CFNX302), region D was larger (Fig. (Fig.3c).3c). The R. tropici amplified strains contained an additional EcoRI fragment that corresponds to the joint fragment (region ZA) of amplification (Fig. (Fig.3d).3d). All of the EcoRI fragments corresponding to regions B, C, D, E, F, and ZA were amplified, while fragments A and Z remained in single copies in the amplified strains. The average level of amplification in strains CFNX303 and CFNX304 was four to five copies of the whole amplicon structure. The amplicon in E. coli and A. tumefaciens does not contain regions A and Z but contains the joint fragment ZA (Fig. (Fig.3e).3e). As expected, fragment ZA hybridizes against the A and Z borders.

FIG. 3
Characterization of AMPRtrCFN299pc60. (a) Overlapping cosmids (indicated by numbers) containing amplicon sequences. (b) Map of amplicon region in wild-type CFN299 showing the locations of different genes. (c) Schematic representation of strain CFNX302 ...

Hybridization of various homologous and heterologous probes against DNA from ordered cosmids, R. tropici wild-type and amplified derivatives, and AMPRtrCFN299pc60 (not shown) led to the identification of several symbiotic genes within the amplicon (Fig. (Fig.3b3b and e). Other gene sequences which were detected in the R. tropici genome but do not form part of the amplicon include nodD3, nodD4, nodL, and nifHDK (not shown).

Determination of AMPRtrCFN299pc60 endpoints.

To investigate the nature of the repeated sequences that border AMPRtrCFN299pc60, we cloned and determined the DNA sequence of region A. Sequence analysis revealed the presence of a novel IS, designated ISRtr1, of 1,364 bp terminated by two 28-bp imperfect inverted repeats (Fig. (Fig.3f).3f). ISRtr1 contains two open reading frames, ORF1 and ORF2, of 651 and 516 nucleotides, respectively. The derived amino acid sequences of these two ORFs shows ≤51% similarity with transposases. The GC content of ISRtr1 is 60.8%, which matches values reported for the Rhizobium genome (56 to 62%), suggesting an endogenous origin. However, BLAST analysis using the GenBank and EMBL databases indicates that ISRtr1 is more closely related to IS elements from gram-positive bacteria such as IS1245 of Mycobacterium avium (12) or IS1164 of Rhodococcus rhodochrous J1 (15).

A PCR product internal to the ISRtr1 sequence was used as a probe to hybridize against Southern blots of EcoRI-digested DNA from the R. tropici wild-type and amplified strains, the isolated AMPRtrCFN299pc60, and an A. tumefaciens transconjugant containing the pSym of CFN299 (not shown). As there is no EcoRI site within the ISRtr1 DNA sequence, we conclude that ISRtr1 or closely related elements are present in at least six copies in the genome. Five are located in the pSym which include the two borders of the described amplicon, one more internal and two external to the amplicon. In addition, the probe revealed the previously identified joint fragment ZA in amplified strains.

Production of Nod factors by Rhizobium amplified derivatives and Agrobacterium bearing AMPRtrCFN299pc60.

Our results confirm the finding (16, 22) that the wild-type CFN299 produces both sulfated and nonsulfated Nod factors whereas the NodP mutant fails to produce sulfated Nod factors (Fig. (Fig.4).4). Surprisingly, the amplified derivative CFNX303 exhibited a TLC pattern different from that of the parental CFNX302 strain. It consists of (i) the clear presence of sulfated Nod factors, albeit in quantities lower than in the wild-type strain, (ii) an evident overproduction of nonsulfated Nod factors, and (iii) the presence of new products in comparison to both wild-type CFN299 and parental CFNX302 strains. HPLC profiles corroborate the TLC results (Fig. (Fig.4B).4B). Interestingly, A. tumefaciens CFNA303 bearing AMPRtrCFN299pc60 was able to excrete nonsulfated Nod factors (Fig. (Fig.4A),4A), suggesting that AMPRtrCFN299pc60 contains sufficient genetic information for Nod factor production.

FIG. 4
Nod factors produced by R. tropici and A. tumefaciens strains. (A) Reverse-phase TLC of 14C-labeled (lanes 1 [induced] and 2 [noninduced]) and 35S-labeled (lanes 3 [induced] and 4 [noninduced]) ...

Nodulation phenotypes.

In comparison to the wild-type CFN299, the strain with a mutation in nodP (CFNX302) formed fewer nodules on cultivar Negro Jamapa and more nodules on cultivar N-8-116 (Fig. (Fig.5),5), in corroboration of previous results (16). Interestingly, in cultivar Negro Jamapa, the amplified strain CFNX303 produced more nodules than the parental strain CFNX302 (Fig. (Fig.5A).5A). However, for only two (II and IV) of four experiments performed were differences significant (P < 0.05). In cultivar N-8-116 (Fig. (Fig.5B),5B), the amplified strain CFNX303 induced significantly more nodules than the wild-type strain in the four experiments performed (P < 0.05). This strain showed a tendency to form more nodules than the parental strain CNFX302, although this increase in nodulation was significant only in experiment III (P < 0.05).

FIG. 5
Nodulation assays with different R. tropici strains and bean cultivars. The average number ± 95% confidence interval of nodules per plant 18 days after inoculation is presented. For each point, 8 to 10 plants were used. (A) Cultivar Negro ...

The nodulation capacity of the A. tumefaciens strain harboring AMPRtrCFN299pc60 (CFNA303) was tested on three different bean cultivars: Negro Jamapa, N-8-116, and BAT-477. In all bean plants tested, strain CFNA303 induced nodules. Typically, A. tumefaciens CFNA303 produced 15 to 20 nodules per plant (not shown), compared to 40 to 70 for the wild-type R. tropici CFN299. Nodules elicited by A. tumefaciens CFNA303 were white and smaller than those induced by Rhizobium strains. Light, scanning, and transmission electron micrographs of nodules formed by A. tumefaciens CFNA303 showed infected plant cells, albeit with fewer bacteria per infected cell than nodules induced by R. tropici wild-type strain (Fig. (Fig.6).6). Furthermore, both contained poly-β-hydroxybutyrate granules (Fig. (Fig.6C).6C).

FIG. 6
Light (magnification, ×40; bar = 200 μm) (A), scanning (×2,000; bar = 10 μm (B), and transmission (×7,500; bar = 1 μm) (C) electron micrographs of bean nodules containing A. tumefaciens CFNA303 harboring ...


In this study, the procedure for identification and mobilization of Rhizobium amplicons was improved. The use of conditional origins of replication (oriV of RK2) and conjugal transfer (oriT of RK2) allowed both the introduction of the GDYN3 element into the Rhizobium genome (in the absence of the transactivator TrfA of oriV of RK2) as well its mobilization into different strains, including A. tumefaciens (in the presence of the trfA gene).

We propose the term “symbiotic amplicons” to refer to amplifiable DNA units of the genome carrying genes essential for symbiosis and suggest the following nomenclature: “AMP” followed by the abbreviated genus (capital letter), species (lowercase letter), and name of the strain, followed by the replicon in which the amplicon is located (“p” for plasmid, followed by the corresponding letter, or “ch” for chromosome) and the size of the amplicon in kilobases. Accordingly, the R. tropici symbiotic amplicon is termed AMPRtrCFN299pc60. The previously reported symbiotic amplicon of R. etli (25) should be termed AMPReCFN42pd120.

AMPRtrCFN299pc60 consists of a 60-kb stretch of DNA flanked by ISRtr1 repeats. ISRtr1 is a novel IS element closely related to IS1245 and IS1164 from gram-positive bacteria (12, 15). Symbiotic genes including nodD1, nodD2, nodABCSUIJ, nodHPQ, nifA, fixLJ, and fixABCX are part of this amplicon. Amplification of AMPRtrCFN299pc60 is probably generated through homologous recombination between ISRtr1 repeats. This model of rearrangement is supported by the presence of the joint fragment in the R. tropici amplified strains and in the amplicon DNA isolated from E. coli. Similar recombination events have been proposed to explain amplification of plasmid and chromosomal DNA regions in different bacteria (2, 13, 35), including pSym regions of R. etli (10, 25).

As the presence of reiterated sequences is a common feature of the Rhizobium genome, we believe that amplicon structures and DNA amplification events may occur in the different Rhizobium species. Actually, the DNA sequence of the symbiotic plasmid of Rhizobium sp. strain NGR234 (11) suggests the existence of several symbiotic amplicons.

The effect of the quality and quantity of Nod factors in regard to nodulation capacity in Rhizobium is complex (24). As previously reported, in R. tropici a mutation in nodP impairs the production of sulfated Nod factors without altering that of the nonsulfated forms, thus decreasing the total amount of Nod factors produced. This, in turn, decreases nodulation in some bean cultivars while improving it in others (reference 16 and Fig. Fig.5).5). Our results show that in amplified strains, Nod factor production clearly increases. Moreover, some sulfated Nod factors are produced. Amplified strains formed more nodules than both wild-type and parental mutant strains. This increment was, however, significant in only some experiments (Fig. (Fig.55).

The presence of sulfated Nod factors in amplified strains was unexpected since mutation in nodP impairs the synthesis of PAPS (3′-phosphoadenosine 5′-phosphosulfate), the activated form of sulfate required for sulfation of the Nod factor core (31, 32). A plausible explanation is that the overproduction of nonsulfated Nod factors may utilize PAPS produced by an alternative pathway such as that described for R. meliloti (33). Actually, in R. tropici CFN299 a chromosomal DNA sequence showing homology with a locus of E. coli involved in the synthesis of PAPS was recently found (17).

Demonstration that the symbiotic amplicon AMPRtrCFN299pc60 contains functional genes essential for Nod factor production and nodulation processes was achieved after its transfer into A. tumefaciens. Transconjugants of A. tumefaciens were able to produce nonsulfated Nod factors like those found in the R. tropici strain containing the GDYN3 element in nodP. Moreover, A. tumefaciens bearing AMPRtrCFN299pc60 induced nodules on beans containing intracellular bacteria. Obviously, these nodules did not fix nitrogen since AMPRtrCFN299pc60 does not contain the structural nifHDK genes.

The fact that our experimental procedure makes the transfer of amplicons into different bacteria possible will facilitate analysis of Nod factor production and its effects on nodulation in both different plants and different bacterial genomic backgrounds. Whether amplicons can also function as transferable elements under natural conditions and increase the flow of plasmid-borne genetic information among bacteria remains to be explored.


We thank J. Vanderleyden and M.-L. Girard for providing gene probes, A. Moreno and J. A. Gama for technical assistance, I. Hernández-Lucas and M. A. Rogel for help in sequencing, and M. Dunn for helpful comments on the manuscript.

This work was supported in part by a grant from CONACYT (México).


1. Altschul S F, Gish W, Miller W, Myers E W, Lipman D J. Basic local alignment search tool. J Mol Biol. 1990;215:403–410. [PubMed]
2. Anderson R P, Roth J R. Tandem genetic duplications in phage and bacteria. Annu Rev Microbiol. 1977;31:473–505. [PubMed]
3. Banfalvi Z, Sakanyan V, Koncz C, Kiss A, Dusha I, Kondorosi A. Location of nodulation and nitrogen fixation genes on a high molecular weight plasmid of Rhizobium meliloti. Mol Gen Genet. 1981;184:318–325. [PubMed]
4. Brewin N J, Beringer J E, Buchanan-Wollaston A V, Johnston A W B, Hirsch P R. Transfer of symbiotic genes with bacteriocigenic plasmids in Rhizobium leguminosarum. J Gen Microbiol. 1980;116:261–270.
5. Dénarié J, Cullimore J. Lipo-oligosaccharide nodulation factors: a minireview new class of signaling molecules mediating recognition and morphogenesis. Cell. 1993;74:951–954. [PubMed]
6. Eckhardt T. A rapid method for the identification of plasmid desoxyribonucleic acid in bacteria. Plasmid. 1978;1:584–588. [PubMed]
7. Fahraeus G. The infection of clover root hairs by nodule bacteria studied by a single glass technique. J Gen Microbiol. 1957;16:374–381. [PubMed]
8. Figurski D H, Helinski D R. Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc Natl Acad Sci USA. 1979;76:1648–1652. [PMC free article] [PubMed]
9. Flores M, González V, Brom S, Martínez E, Piñero D, Romero D, Dávila G, Palacios R. Reiterated DNA sequences in Rhizobium and Agrobacterium. J Bacteriol. 1987;169:5782–5788. [PMC free article] [PubMed]
10. Flores M, Brom S, Stepkowski T, Girard M L, Dávila G, Romero D, Palacios R. Gene amplification in Rhizobium: identification and in vivo cloning of discrete amplifiable DNA regions (amplicons) from Rhizobium leguminosarum biovar phaseoli. Proc Natl Acad Sci USA. 1993;90:4932–4936. [PMC free article] [PubMed]
11. Freiberg C, Fellay R, Bairoch A, Broughton W J, Rosenthal A, Perret X. Molecular basis of symbiosis between Rhizobium and legumes. Nature. 1997;387:394–401. [PubMed]
12. Guerrero C, Bernasconi C, Burki D, Bodmer T, Telenti A. A novel insertion element from Mycobacterium avium, IS1245, is a specific target for analysis of strain relatedness. J Clin Microbiol. 1995;33:304–307. [PMC free article] [PubMed]
13. Hill C W, Grafstrom R H, Hanish W B, Hillman B S. Tandem duplications resulting from recombination between ribosomal RNA genes in Escherichia coli. J Mol Biol. 1977;116:407–428. [PubMed]
14. Hynes M F, McGregor N F. Two plasmids other than the nodulation plasmid are necessary for formation of nitrogen-fixing nodules in Rhizobium leguminosarum. Mol Microbiol. 1990;4:567–574. [PubMed]
15. Komeda H, Kobayashi M, Shimizu S. Characterization of the gene cluster of high-molecular-mass nitrile hydratase (H-NHase) induced by its reaction product in Rhodococcus rhodochrous J1. Proc Natl Acad Sci USA. 1996;93:4267–4272. [PMC free article] [PubMed]
15a. Koncz, C. Unpublished data.
16. Laeremans T, Caluwaerts I, Verreth C, Rogel M A, Vanderleyden J, Martínez-Romero E. Isolation and characterization of the Rhizobium tropici Nod factor sulfation genes. Mol Plant-Microbe Interact. 1996;9:492–500. [PubMed]
17. Laeremans, T., E. Martínez-Romero, and J. Vanderleyden. Isolation and sequencing of a second Rhizobium tropici CFN299 genetic locus that contains genes homologous to amino acid sulfate activation genes. DNA Sequence, in press. [PubMed]
18. Marsh J L, Erfle M, Wykes E J. The pIC plasmid and phage vectors with versatile cloning sites for recombinant selection by insertional inactivation. Gene. 1984;32:481–485. [PubMed]
19. Martínez-Romero E, Segovia L, Mercante F M, Franco A A, Graham P, Pardo M A. Rhizobium tropici, a novel species nodulating Phaseolus vulgaris L. beans and Leucaena sp. trees. Int J Syst Bacteriol. 1991;41:417–426. [PubMed]
20. Mavingui P, Flores M, Romero D, Martínez-Romero E, Palacios R. Generation of Rhizobium strains with improved symbiotic properties by random DNA amplification (RDA) Nat Biotechnol. 1997;15:564–569. [PubMed]
21. Norrander J, Kempe T, Messing J. Construction of improved M13 vectors using oligodeoxynucleo-directed mutagenesis. Gene. 1983;26:101–106. [PubMed]
22. Poupot R, Martínez-Romero E, Promé J-C. Nodulation factors from Rhizobium tropici are sulfated or nonsulfated chitopentasaccharides containing an N-methyl-N-acetylglucosaminyl terminus. Biochemistry. 1993;32:10430–10435. [PubMed]
23. Quandt J, Hynes M F. Versatile suicide vectors which allow direct selection for gene replacement in Gram-negative bacteria. Gene. 1993;127:15–21. [PubMed]
24. Relic′ B, Staehelin C, Fellay R, Jabbouri S, Boller T, Broughton W J. Do Nod-factor levels play role in host-specificity? In: Kiss G B, Endre G, editors. Proceedings of the First European Congress on Nitrogen Fixation. Szeged, Hungary: Officina Press Szed; 1994. pp. 69–75.
25. Romero D, Brom S, Martínez-Salazar J, Girard M L, Palacios R, Dávila G. Amplification and deletion of a nod-nif region in the symbiotic plasmid of Rhizobium phaseoli. J Bacteriol. 1991;173:2435–2441. [PMC free article] [PubMed]
26. Romero D, Martínez-Salazar J, Girard M L, Brom S, Dávila G, Palacios R. Discrete amplifiable regions (amplicons) in the symbiotic plasmid of Rhizobium etli CFN42. J Bacteriol. 1995;177:973–980. [PMC free article] [PubMed]
27. Romero D, Dávila G, Palacios R. The dynamic genome of Rhizobium. In: De Bruijn F J, Lupski J R, Weinstock G M, editors. Bacterial genomes: physical structure and analysis. New York, N.Y: Chapman and Hall; 1997. pp. 153–161.
28. Rosenberg C, Boistard P, Dénarié J, Casse-Delbart F. Genes controlling early and late functions in symbiosis are located on a megaplasmid in Rhizobium meliloti. Mol Gen Genet. 1981;184:326–333. [PubMed]
29. Rosenberg C, Huguet T. The pAtC58 plasmid of Agrobacterium tumefaciens is not essential for tumor induction. Mol Gen Genet. 1984;196:533–536.
30. Schultze M, Kondorosi E, Ratet P, Buiré M, Kondorosi A. Cell and molecular biology of Rhizobium-plant interactions. Int Rev Cytol. 1994;156:1–74.
31. Schwedock J S, Long S R. ATP sulphurylase activity of the nodP and nodQ gene products of Rhizobium meliloti. Nature. 1990;348:644–647. [PubMed]
32. Schwedock J S, Liu C, Leyh T S, Long S R. Rhizobium meliloti NodP and NodQ form a multifunctional sulfate-activating complex requiring GTP for activity. J Bacteriol. 1994;176:7055–7064. [PMC free article] [PubMed]
33. Schwedock J S, Long S R. Rhizobium meliloti genes involved in sulfate activation: the two copies of nodPQ and a new locus, saa. Genetics. 1992;132:899–909. [PMC free article] [PubMed]
34. Simon R, Priefer U, Pühler A. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram-negative bacteria. Bio/Technology. 1983;1:784–791.
35. Spies T, Laufs R. Circularized copies of amplifiable resistance genes from Haemophilus influenzae plasmids. J Bacteriol. 1983;156:1263–1267. [PMC free article] [PubMed]
35a. Valencia, E., and D. Romero. Unpublished data.
36. Vandenbosch K A, Noel K D, Kaneko Y, Newcomb E H. Nodule initiation elicited by noninfective mutants of Rhizobium phaseoli. J Bacteriol. 1985;162:950–959. [PMC free article] [PubMed]

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