Department of Applied Chemistry and Microbiology
Institute of Biotechnology, University of Helsinki, Helsinki, Finland
Department of Genetics, Harvard Medical School, and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
![]() |
Abstract |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
![]() |
Introduction |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Rhizobial classification has traditionally been based on a "cross-inoculation concept," which means that the early rhizobial taxonomy was based to a large degree on host specificity (Fred, Baldwin, and McCoy 1932
). Thus, the symbiotic nodulation (nod) genes of rhizobia, which are the determinants of the host range, had an important role in rhizobial taxonomy. More recently, phylogenetic analyses combined with molecular methods, such as DNA hybridization, DNA sequencing, and typing methods (Vandamme et al. 1996
), have provided tools to generate more reliable classifications. At present, the sequencing of 16S rRNA genes is one of the basic methods used for bacterial classification (Graham et al. 1991
; Young and Haukka 1996
; Terefework et al. 1998
). As a result, the taxonomy of rhizobia is undergoing rapid revision.
The rhizobial genes involved in the construction of the symbiotic organ in plant roots or stems, the nodule, are designated as nodulation (nod) genes. The transcription of the nodulation genes is induced through the regulatory nodD genes, which mediate host specificity by activating nod operons in response to various flavonoid compounds derived from legume hosts (Horvath et al. 1987
; Spaink et al. 1987
; Györgypal, Iyer, and Kondorosi 1988
; Honma, Asomaning, and Ausubel 1990
). The expression of nod genes results in the synthesis of extracellular bacterial compounds, the Nod factors (Carlson, Price, and Stacey 1995
; van Rhijn and Vanderleyden 1995
). These factors act as signals, which, in the appropriate host plant, elicit the first symptoms of nodule formation, such as deformation of root hairs, formation of infection threads, and cell division in the root cortex (Lerouge et al. 1990
).
Common nodulation genes nodABC and nodIJ are involved in the synthesis of the basic oligosaccharide core of the Nod factors. The highly conserved nature of the common nodulation genes among rhizobial species is clearly indicated by sequence data available from various rhizobia (for references, see the accession numbers in table 1
). However, in spite of their high sequence similarity, the common nod genes are not functionally conserved among rhizobial species (Debelle et al. 1996
). The Nod factors are acetylated with fatty acids either from the general lipid metabolism or from a specific
,ß-unsaturated fatty acid pool (Yang et al. 1999). The nodA gene, which codes for an acyltransferase and determines the type of the N-acyl substitution transferred into the oligosaccharide backbone of the Nod factor, plays a critical role in making this distinction. Thereby, the function of the NodA protein specifies the Nod factor structure and the host range (Ritsema et al. 1996
). Because the bacterial Nod factor is a key signal molecule in the initiation of the plant root nodule, it is expected to evolve under constraints imposed by interaction with the host plant. To date, evolution of the Nod factor under such constraint has not been clearly demonstrated.
|
The major questions about the evolution of nodulation concern the origin of rhizobial nod genes, the relationship between the phylogeny of the nod genes and that derived from genomic sequences, and the influence of the host plant on nod gene evolution (Young 1993, 1994
; Dobert, Breil, and Triplett 1994
; Young and Haukka 1996
; Doyle 1998
).
In this work, we describe the cloning, sequencing, and structure of the common nod region of Rhizobium galegae, a rhizobial species with a peculiar position in the Agrobacterium clade based on 16S rRNA sequence analyses (Lindström 1989
; Willems and Collins 1993
; Young and Haukka 1996
). We used phylogenetic analysis to examine the evolutionary relationships of the nodulation genes to the bacterial and the host plant genomes.
![]() |
Materials and Methods |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
|
Cloning and Identification of the Common nod Region
The construction of the R. galegae HAMBI 1174 clone library has been described previously (Suominen et al. 1999
). To clone the common nodulation genes, the cosmid library was conjugated into two mutants of Sinorhizobium meliloti, Rm1126 and Rm1027, both carrying a mutated nodC gene (Buikema et al. 1983
). Conjugations were conducted according to protocols described by Ruvkun and Ausubel (1981)
, with pRK2013 as a helper plasmid. Transconjugants were used in en masse infection of alfalfa as described by Marvel et al. (1985)
. After 30 days, bacteria from the nodules showing activity in acetylene reduction measurements (Lindström 1984
) were isolated, and their plasmid content was examined by EcoRI digestion. A 28-kb plasmid, pRg30, which carried a 9.2-kb EcoRI fragment dominating in restriction profiles, gave a positive reaction in a hybridization assay with the common nod probe pRmJ1 from S. meliloti and was chosen for further study. A restriction map of pRg30 was constructed. The location of the nodulation genes in pRg30 was investigated by hybridizations using internal fragments of S. meliloti nodABCD and nodD genes from plasmid pRmSL42 and a synthetic nod promoter sequence, nod-box, as probes.
To verify the functionality of the R. galegae common nodulation genes, site-directed Tn5 mutagenesis was performed in the nod gene region by the method of de Bruijn and Lupski (1984)
, and the insertion sites were mapped by restriction endonucleases. For marker exchange, pRg33, a 6-kb subclone of pRg30 (see fig. 1 ), carrying a Tn5 in nodABC, was conjugated into R. galegae HAMBI 1174. Selection for strains in which Tn5 had recombined with the R. galegae genome was carried out following Ruvkun and Ausubel (1981)
. The correct location of the Tn5 insertion was verified by DNA hybridization.
|
Phylogenetic Analysis of nod Genes
Bacterial nod DNA sequences used for the phylogenetic studies are listed in table 1
, and the accession numbers for 16S rRNA and legume internal transcribed sequence (ITS) sequences are shown in table 3
. For the nod DNA sequences, only the coding regions were used. DNA sequences were aligned with the program PILEUP (Wisconsin Package, version 10.0; Genetics Computer Group, Madison, Wis.) or with CLUSTAL W, version 1.7 (Thompson, Higgins, and Gibson 1994
), using an identity matrix, a gap weight of 8, and a gap length weight of 0.1. Amino acid sequences were aligned with the same programs using a Blosum82 protein weight matrix, a gap weight of 12, and a gap length weight of 0.5. The nod DNA alignments were checked by eye and corrected to avoid alignments with disrupted reading frames. Trees were constructed from the data by maximum parsimony and neighbor joining (NJ) using programs from the PHYLIP (Felsenstein 1993
) and Treecon (Van de Peer and De Wachter 1994
) packages and the GCG implementation of PAUP* (Wisconsin package). Heuristic searches were utilized in parsimony analyses due to the large number of taxa examined. Branch swapping was done by tree bisection-reconnection. For NJ analyses, distance measures were employed using a Kimura two-parameter correction for multiple hits and a transition/transversion ratio of 2. Bootstrap analyses with 1,000 replicates were performed to examine the relative support for relationships in the resultant topologies. Rhizobium trees were rooted with respect to Azorhizobium caulinodans, which, according to polyphasic taxonomic studies (Vandamme et al. 1996
), is the most distant species among the rhizobia included in the analyses (Dreyfus, Garcia, and Gillis 1988
). A test of phylogenetic congruence among phylogenies inferred for the nod genes, the 16S rRNA genes, and the host plants was conducted using TreeMap (Page 2000
). TreeView (Page 1996
) was used to prepare illustrations of the trees.
|
![]() |
Results |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Sequencing of the Common Nodulation Region
The sequence data verified the restriction sites previously detected by restriction analysis and revealed the existence of six major open reading frames in the pRg33 region (fig. 1
). The organization of the common nod gene region of R. galegae was similar to that of S. meliloti and Rhizobium leguminosarum, with nodIJ downstream of nodABC and the regulatory nodD gene closely linked to the common nod operon. These genes code for the NodD, NodA, NodB, NodC, NodI, and NodJ proteins. The highest protein sequence identities with known rhizobial nodulation proteins were 74% for NodA with R. leguminosarum biovar trifolii, 65% for NodB with R. leguminosarum biovar viciae, 70% for NodC with Rhizobium sp. NGR234, 74% for NodI and NodJ with R. leguminosarum biovar viciae, and 79% for NodD with both S. meliloti and R. leguminosarum biovar viciae. The percentages were measured over the total length of the protein. The organization of the common nod gene region was similar to that of R. leguminosarum and S. meliloti, with nodIJ downstream of nodABC (Rossen, Johnston, and Downie 1984
; Egelhoff et al. 1985
; Surin et al. 1990
). The regulatory nodD gene was located adjacent to the common nod operon and translated from the opposite strand of a stretch of DNA lying 248 bp upstream of nodA (fig. 1
).
Phylogenetic Analysis of the Sequences
Phylogenetic analyses of the DNA sequences were conducted using the R. galegae nod genes sequenced in this study and corresponding sequences published in the EMBL database (table 1
). Phylogenetic trees obtained from maximum-likelihood, parsimony, and neighbor-joining analyses were identical with respect to the clustering of the main groups. The inferred phylogeny of complete nodA gene sequences at both the DNA (fig. 2A
) and the protein (fig. 2B
) levels grouped R. galegae HAMBI 1174 with S. meliloti and R. leguminosarum, in contradiction to what would be expected from previous work based on 16S rRNA genes (Willems and Collins 1993
), which grouped R. galegae with Agrobacterium. The bootstrap support for this group was 87% in analyses based on amino acid sequences (fig. 2B
). The observed grouping of R. galegae nodA genes with S. meliloti and R. leguminosarum nodA genes seemed to follow previously published hypotheses of host plant phylogeny (Polhill 1981
; Doyle, Lavin, and Bruneau 1992
; Doyle et al. 1997
).
|
The comparison of the bacterial nodA gene/host plant phylogeny to the bacterial nodA gene/bacterial 16S rRNA phylogeny performed with TreeMap was indicative of a high congruence between the nodA gene and host plant ITS-based phylogeny but not the 16S rRNA phylogeny. Also, visual inspection of both tree pairs, or "tanglegrams" (fig. 3 ), unveils a major difference in the position of the R. galegae grouping. In the host tanglegram, R. galegae clearly groups with S. meliloti and R. leguminosarum (fig. 3B ), whereas this is not the case in the 16S rRNA tanglegram (fig. 3A ). This difference is taken as evidence of lateral transfer of the nodA gene into R. galegae from a common ancestor of S. meliloti and R. leguminosarum.
|
![]() |
Discussion |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
In this work, we present the organization of the symbiotic nod genes in R. galegae and confirm that the phylogeny of the nod genes is clearly different from the phylogeny based on the 16S rRNA genes. This difference, together with the fact that many nonsymbiotic bacteria are intermingled with rhizobia in the phylogenetic tree of the alpha subdivision of the Proteobacteria, implies that all rhizobia did not inherit their nod genes directly from their ancestor (Young and Haukka 1996
; Terefework et al. 1999
).
The common nodulation genes that we identified from R. galegae have a structure and orientation similar to those of R. leguminosarum and S. meliloti (Rossen, Johnston, and Downie 1984
; Egelhoff et al. 1985
; Surin et al. 1990
). In these rhizobia, the nodDABCIJ genes form a cassette located on a plasmid, whereas in other rhizobia the nod genes are scattered throughout the genome, and some additional nodulation genes may be inserted in the common nod region (Lindström 1989
; Selenska-Trajkova et al. 1990
; Lindström et al. 1995
; Freiberg et al. 1997
). The similarity of organization of the nod genes of R. galegae, R. leguminosarum, and S. meliloti suggests that these genes originate from the same evolutionary source. However, as R. galegae is rather distant from R. leguminosarum and S. meliloti in the 16S rRNAbased phylogeny, only lateral transfer of nodulation genes could account for this high similarity. The concept of lateral transfer is given further support by our phylogenetic analyses.
Our phylogenetic study, which was based on parsimony and neighbor-joining analyses of complete, aligned nodA, nodB, and nodC nucleotide and amino acid sequences, provided a well-supported estimate of nod gene phylogeny. The R. galegae Nod protein sequences were most closely related to those of R. leguminosarum and S. meliloti biovars viciae and trifolii in spite of the distant taxonomic position of R. galegae relative to other Rhizobium species. Rhizobium leguminosarum and S. meliloti are fast-growing rhizobia with a fairly narrow host range. They infect the temperate legume tribes Vicieae and Trifolieae, with a similar infection type and an indeterminate nodule structure. The host tribe of R. galegae, Galegeae, is closely related to Vicieae and Trifolieae (Doyle 1998
). Thus, it seems probable that these legumes share a similar receptor system for Nod factors, the symbiotic signals from rhizobia. Therefore, it is likely that the host constrains the evolution of the nod region by selecting against changes that prevent host infection.
Several authors have discussed the role of the host plant in nod gene evolution. While some think that there is little correlation between rhizobial and plant phylogenies (Young and Johnston 1989
; Doyle 1994, 1998
), others suggest that the rhizobial nod gene phylogeny might be congruent with the phylogeny of the host plants while the bacterial phylogeny as a whole would not (Dobert, Breil, and Triplett 1994
). Indeed, Kaijalainen and Lindström (1989)
studied several strains of R. galegae by analysis of restriction fragment length polymorphism and showed that the symbiotic (common nod and nifHDK) probes grouped the bacteria according to the host plant Galega officinalis or G. orientalis, whereas the constitutive (hemA, glnA, ntrC, and recA) probes did not. Our study shows that common nod genes from R. galegae group according to host plant. However, differences in function of the nod genes are expected to be reflected in how strictly they follow the host plant phylogeny rather than the 16S rRNAbased bacterial phylogeny.
The Nod factors are acetylated with fatty acids either from the general metabolism or, in a subset of rhizobial strains, from a polyunsaturated fatty acid pool (Yang et al. 1999
). The nodA gene determines the type of the N-acyl substitution of the Nod factor and therefore plays a crucial role in host plant recognition (Ritsema et al. 1996
; Yang et al. 1999
). The Nod factors produced by R. leguminosarum and S. meliloti both have polyunsaturated fatty acid chains (Lerouge et al. 1990
; Spaink et al. 1991
; Spaink, Wijfjes, and Lugtenberg 1995
). Rhizobium galegae has been shown to have the same type of fatty acid substitution (Yang et al. 1999
). Moreover, we found that nodA was the nod gene that showed the most strict hostlike phylogeny. Taken together, our results clearly demonstrate that the Nod factor in R. galegae has evolved under strong constraint imposed by the host plant interaction following a historically more ancient lateral gene transfer event.
Several questions remain unanswered. Our studies were based on the finding that the R. galegae nodDABCIJ genes form a plasmid-borne cassette and are related to similar cassettes on nonrelated bacterial species that infect related host plants. This incongruence, most apparent for the nodA gene, implies that the common nod genes have evolved through lateral transfer between major chromosomal subdivisions. However, further studies are required to identify the primary unit of evolution: the cassette as a whole or, for example, the nodA gene, with the other nod genes showing similar, albeit less obvious, evolution simply due to some kind of "hitchhiking" effect. Moreover, further study will be needed to identify additional putative gene transfer events that may have led to the present state of nod gene organization in symbiotic rhizobia.
![]() |
Acknowledgements |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
![]() |
Footnotes |
---|
1 Keywords: legumes
Rhizobium
phylogeny
nodulation genes
host constraint
2 Address for correspondence and reprints: Leena Suominen, Department of Applied Chemistry and Microbiology, Division of Microbiology, P.O. Box 56, Biocenter 1, FIN-00014, University of Helsinki, Finland. leena.suominen{at}helsinki.fi
.
![]() |
literature cited |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Beringer, J. E. 1974. R factor transfer in Rhizobium leguminosarum. J. Gen. Microbiol. 84:188198
Buikema, W. J., S. R. Long, S. E. Brown, R. C. Van Den Bos, C. Earl, and F. M. Ausubel. 1983. Physical and genetic characterization of Rhizobium meliloti symbiotic mutants. J. Mol. Appl. Genet. 2:249260[Medline]
Carlson, R. W., N. J. Price, and G. Stacey. 1995. The biosynthesis of rhizobial lipo-oligosaccharide nodulation signal molecules. Mol. Plant Microbe Interact. 7:684695[ISI]
de Bruijn, F. J., and J. R. Lupski. 1984. The use of transposon Tn5 mutagenesis in the rapid generation of correlated physical and genetic maps of DNA segments cloned into multicopy plasmids. Gene 27:131149
de Lajudie, P., E. Laurent-Fulele, A. Willems, U. Tork, R. Coopman, M. D. Collins, K. Kersters, B. Dreyfus, and M. Gillis. 1998.Description of Allorhizobium undicola gen. nov., sp. nov., for nitrogen-fixing bacteria, efficiently nodulating Neptunia natans in Senegal. Int. J. Syst. Bacteriol. 48:12771290
Dear, S., and R. Staden. 1991. A sequence assembly and editing program for efficient management of large projects. Nucleic Acids Res. 19:39073911[Abstract]
Debelle, F., C. Plazanet, P. Roche, C. Pujol, A. Savagnac, C. Rosenberg, J. C. Prome, and J. Denarie. 1996. The NodA proteins of Rhizobium meliloti and Rhizobium tropici specify the N-acylation of Nod factors by different fatty acids. Mol. Microbiol. 22:303314[ISI][Medline]
Ditta, G., S. Stanfield, D. Corbin, and D. Helinski. 1980. Broad host range DNA cloning system for gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc. Natl. Acad. Sci. USA 7:73477351
Dobert, R. C., B. T. Breil, and E. W. Triplett. 1994. DNA sequence of the common nodulation genes of Bradyrhizobium elkanii and their phylogenetic relationship to those of other nodulating bacteria. Mol. Plant Microbe Interact. 7:564572[ISI][Medline]
Doyle, J. J. 1994. Phylogeny of the Legume family: an approach to understanding the origins of nodulation. Annu. Rev. Ecol. Syst. 25:325349[ISI]
. 1998. Phylogenetic perspectives on nodulation: evolving views of plants and symbiotic bacteria. Trends Plant Sci. 3:473478[ISI]
Doyle, J. J., J. L. Doyle, J. A. Ballenger, E. E. Dickson, T. Kajita, and O. Ohashi. 1997. A phylogeny of the chloroplast gene rbcL in the Leguminosae: taxonomic correlations and insights into the evolution of nodulation. Am. J. Bot. 84:541554[Abstract]
Doyle, J. J., M. Lavin, and A. Bruneau. 1992. Contributions of molecular data to papilionoid legume systematics. Pp. 223251 in P. S. Soltis, D. E. Soltis, and J. J. Doyle, eds. Molecular systematics of plants. Chapman and Hall, New York, London
Dreyfus, B. L., J. L. Garcia, and M. Gillis. 1988. Characterization of Azorhizobium caulinodans gen. nov., sp. nov., a stem nodulating nitrogen fixing bacterium isolated from Sesbania rostrata. Int. J. Syst. Bacteriol. 38:8998
Egelhoff, T. T., R. F. Fisher, T. W. Jacobs, J. T. Mulligan, and S. R. Long. 1985. Nucleotide sequence of Rhizobium meliloti 1021 nodulation genes: nodD is read divergently from nodABC. DNA 4:241248
Felsenstein, J. 1993. PHYLIP (phylogeny inference package). Version 3.5c. Distributed by the author, Department of Genetics, University of Washington, Seattle (http://evolution.genetics.washington.edu/phylip/phylip.html)
Fred, E. B., I. L. Baldwin, and E. McCoy. 1932. Root nodule bacteria and leguminous plants. University of Wisconsin, Madison
Freiberg, C., R. Fellay, A. Bairoch, W. J. Broughton, A. Rosenthal, and X. Pierret. 1997. Molecular basis of symbiosis between Rhizobium and legumes. Nature 387:394401
Friedman, A. M., S. R. Long, S. E. Brown, W. J. Buikema, and F. M. Ausubel. 1982. Construction of a broad host range cosmid cloning vector and its use in the genetic analysis of Rhizobium mutants. Gene 18:289296
Graham, P. H., M. J. Sadowsky, H. H. Keyser et al. (11 co-authors). 1991. Proposed minimal standards for the description of new genera and species of root- and stem-nodulating bacteria. Int. J. Syst. Bacteriol. 41:582587
Györgypal, Z., N. Iyer, and A. Kondorosi. 1988. Three regulatory nodD alleles of diverged flavonoid specificity are involved in host-dependent nodulation by Rhizobium meliloti. Mol. Gen. Genet. 212:8592
Györgypal, Z., G. B. Kiss, and A. Kondorosi. 1991. Transduction of plant signal molecules by the Rhizobium NodD proteins. Bioessays 13:575581
Hames, B. D., and S. J. Higgins. 1985. Nucleic acid hybridization: a practical approach. IRL Press, Oxford, England
Honma, M. A., M. Asomaning, and F. M. Ausubel. 1990. Rhizobium meliloti nodD genes mediate host specific activation of nodABC. J. Bacteriol. 172:901911[ISI][Medline]
Horvath, B., C. W. B. Bachem, J. Schell, and A. Kondorosi. 1987. Host specific regulation of nodulation genes in Rhizobium is mediated by a plant signal, interacting with the nodD gene product. EMBO J. 6:841848[ISI]
Jacobs, T. W., T. T. Egelhoff, and S. R. Long. 1985. Physical and genetic map of Rhizobium meliloti nodulation gene region and nucleotide sequence of nodC. J. Bacteriol. 162:469476[ISI][Medline]
Kaijalainen, S., and K. Lindström. 1989. Restriction fragment length polymorphism of Rhizobium galegae strains. J. Bacteriol. 171:55615566[ISI][Medline]
Lerouge, P., P. Roche, C. Faucher, F. Maillet, G. Truchet, J. C. Prome, and J. Denarie. 1990. Symbiotic host specificity of Rhizobium meliloti is determined by a sulphated and acylated glucosamine oligosaccharide signal. Nature 344:781784
Lindström, K. 1984. Analysis of factors affecting in situ nitrogenase (C2H2) activity of Galega orientalis, Trifolium pratense, and Medigago sativa in temperate conditions. Plant Soil 79:329341
. 1989. Rhizobium galegae, a new species of legume root nodule bacteria. Int. J. Syst. Bacteriol. 39:365367
Lindström, K., and S. Lehtomäki. 1988. Metabolic properties, maximum growth temperature and phage typing as means of distinguishing Rhizobium sp. (Galega) from other fast growing rhizobia. FEMS Microbiol. Lett. 50:277287
Lindström, K., L. Paulin, C. Roos, and L. Suominen. 1995. Nodulation genes of Rhizobium galegae. Pp. 365370 in I. A. Tikhonovich, N. A. Provorov, V. I. Romanov, and W. E. Newton, eds. Nitrogen fixation: fundamentals and applications. Kluwer, the Netherlands
Lindström, K., M. L. Sarsa, J. Polkunen, and P. Kansanen. 1985. Symbiotic nitrogen fixation of Rhizobium (Galega) in acid soils, and its survival in soil under acid and cold stress. Plant Soil 87:293302
Maniatis, T., E. F. Fritsch, and J. Sambrook. 1982. Molecular cloning. A laboratory manual. Cold Spring Harbor Laboratory Press, N.Y
Martinez-Romero, E., and J. Caballero-Mellado. 1996. Rhizobium phylogenies and bacterial genetic diversity. Crit. Rev. Plant Sci. 15:113140[ISI]
Marvel, D. J., G. Kuldau, A. Hirsch, E. Richards, J. G. Torrey, and F. M. Ausubel. 1985. Conservation of nodulation genes between Rhizobium meliloti and a slow growing Rhizobium strain that nodulates a nonlegume host. Proc. Natl. Acad. Sci. USA 82:58415845
Meade, H. M., S. R. Long, G. B. Ruvkun, S. E. Brown, and F. M. Ausubel. 1982. Physical and genetic characterization of symbiotic and auxotrophic mutants of Rhizobium meliloti induced by transposon Tn5 mutagenesis. J. Bacteriol. 149:114122[ISI][Medline]
Mercado-Blanco, J., and N. Toro. 1996. Plasmids in rhizobia: the role of nonsymbiotic plasmids. Mol. Plant Microbe Interact. 9:535545[ISI]
Page, R. D. M. 1994. Parallel phylogenies: reconstructing the history of host-parasite assemblages. Cladistics 10:155173
. 1996. TreeView: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12:357358[Medline]
. 2000. TreeMap is an experimental program for comparing host and parasite trees. It is available for both Windows and Apple Macs on the World Wide Web at http://taxonomy.zoology.gla.ac.uk/rod/treemap.html
Polhill, R. M. 1981. Papilionoideae. Pp. 191208 in R .M. Polhill and P. H. Raven, eds. Advances in legume systematics. Part 1. Royal Botanic Gardens, Kew, England
Provorov, N. A. 1994. The interdependence between taxonomy of legumes and specificity of their interaction with rhizobia in relation to evolution of the symbiosis. Symbiosis 17:183200
Ritsema, T., A. M. H. Wijfjes, B. J. J. Lugtenberg, and H. Spaink. 1996. Rhizobium nodulation protein NodA is a host specific determinant of the transfer of fatty acids in Nod factor biosynthesis. Mol. Gen. Genet. 251:4451[ISI][Medline]
Rossen, L., A. B. W. Johnston, and J. A. Downie. 1984. DNA sequence of the Rhizobium leguminosarum nodulation genes nodAB and C required for root hair curling Nucleic Acids Res. 12:94979508
Rostas, K., E. Kondorosi, B. Horvath, A. Simoncsits, and A. Kondorosi. 1986. Conservation of extended promoter regions of nodulation genes in Rhizobium. Proc. Natl. Acad. Sci. USA 83:17571761
Ruvkun, G. B., and F. M. Ausubel. 1981. A general method for site directed mutagenesis in prokaryotes. Nature 289:8588
Selenska-Trajkova, S., G. Radeva, L. Gigova, and K. Markov. 1990. Localization of nif genes on large plasmids in Rhizobium galegae. Lett. Appl. Microbiol. 11:7376
Spaink, H. P., D. M. Sheeley, A. A. N. van Brussel, J. Glushka, W. S. York, T. Tak, O. Geiger, E. P. Kennedy, V. N. Reinhold, and B. J. J. Lugtenberg. 1991. A novel highly unsaturated fatty acid moiety of lipo-oligosaccharide signals determines host specificity of Rhizobium. Nature 354:125130
Spaink, H. P., C. A. Wijffelman, E. Pees, R. H. Okker, and B. J. J. Lugtenberg. 1987. Rhizobium nodulation gene nodD as a determinant of host specificity. Nature 328:337340
Spaink, H. P., A. H. M. Wijfjes, and B. J. J. Lugtenberg. 1995. Rhizobium NodI and NodJ proteins play a role in the efficiency of secretion of lipochitin oligosaccharides. J. Bacteriol. 177:62766281[Abstract]
Suominen, L., L. Paulin, A. Saano, A.-M. Saren, E. Tas, and K. Lindström. 1999. Identification of nodulation promoter (nod-box) regions of Rhizobium galegae. FEMS Microbiol. Lett. 177:217223
Surin, B. P., J. M. Watson, W. D. O. Hamilton, A. Economou, and A. Downie. 1990. Molecular characterization of the nodulation gene, nodT, from two biovars of Rhizobium leguminosarum. Mol. Microbiol. 4:245252
Terefework, Z., G. Lortet, L. Suominen, and K. Lindström. 1999. Molecular evolution of interactions between rhizobia and their legume hosts. In E. Triplett, ed. Nitrogen fixation in prokaryotes: molecular and cellular biology. Horizon Scientific Press, Norfolk, England
Terefework, Z., G. Nick, S. Suomalainen, L. Paulin, and K. Lindström. 1998. Phylogeny of Rhizobium galegae with respect to other rhizobia and agrobacteria. Int. J. Syst. Bacteriol. 48:349356
Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:46734680[Abstract]
Ueda, T., Y. Suga, N. Yahiro, and T. Matsuguchi. 1995. Phylogeny of Sym plasmids of rhizobia by PCR-based sequencing of a nodC segment. J. Bacteriol. 177:468472[Abstract]
Van de Peer, Y., and R. De Wachter. 1994. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Appl. Biosci. 10:569570[Medline]
van Rhijn, P., and J. Vanderleyden. 1995. The Rhizobium-plant symbiosis. Microbiol. Rev. 59:124142[Abstract]
Vandamme, P., B. Pot, M. Gillis, P. de Vos, K. Kerstens, and J. Swings. 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60:407438[Abstract]
Vincent, J. M. 1970. A manual for the practical study of root-nodule bacteria. International biological program handbook 15. Blackwell Scientific Publications, Oxford, England
Wang, E. T., and E. Martinez-Romero. 2000. Phylogeny of root and stem nodule bacteria associated with Legumes. Pp. 177186 in E. W. Triplett, ed. Prokaryotic nitrogen fixation: a model system for analysis of a biological process. Horizon Scientific Press, Wymondham, England
Wernegreen, J. J., and M. A. Riley. 1999. Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages. Mol. Biol. Evol. 16:98113[Abstract]
Willems, A., and M. D. Collins. 1993. Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 43:305313[Abstract]
Yang, G. P., F. Debelle, A. Savagnac et al. (12 co-authors). 1999. Structure of the Mesorhizobium huakuii and Rhizobium galegae Nod factors: a cluster of phylogenetically related legumes are nodulated by rhizobia producing Nod factors with ,ß-unsaturated N-acyl substitutions. Mol. Microbiol. 34:227237[ISI][Medline]
Young, J. P. W. 1993. Molecular phylogeny of rhizobia and their relatives. Pp. 587592 in R. Palacios, J. Mora, and W. E. Newton, eds. New horizons in nitrogen fixation. Kluwer, Dordrecht, the Netherlands
. 1994. All those new names: an overview of the molecular phylogeny of plant associated bacteria. Pp. 7380 in M. J. Daniels, J. A. Downie, and A. E. Osbourn, eds. Advances in molecular genetics of plant-microbe interactions. Vol. 3. Kluwer, Dordrecht, The Netherlands
Young, J. P. W., and K. Haukka. 1996. Diversity and phylogeny of rhizobia. New Phytol. 133:8794[ISI]
Young, J. P. W., and A. W. B. Johnston. 1989. The evolution of specificity in the legume-Rhizobium symbiosis. Trends Ecol. Evol. 4:341349[ISI]