Chapter 12 : The Symbiotic Plasmids of the

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The , with around 18,000 species, is the largest plant family on Earth; its ecological success owes much to the existence of nitrogen-fixing symbioses with prokaryotes. These symbioses occur mainly with members of the family (belonging to the a-proteobacteria). Clearly, research in the molecular biology of rhizobia- legume interactions has illuminated the ways in which bacteria and eukaryotes interact in a symbiotic process. However, this research also showed, almost from the start, the existence of novel forms of genome organization in prokaryotes, such as the finding of multiple large plasmids. Conversely, elimination of the pSym impairs both nodulation and nitrogen fixation of the original bacterial strain. Plasmids p42c, p42e, and p42f influence successful competitiveness between strains for nodulation, while p42f is needed for nitrogen fixation; only the self-conjugative plasmid p42a appears to be dispensable for symbiosis. As everything in biology, the current revolution in genomics has changed the way in which one addresses these problems. On the backbone, genes for nodulation are located in three noncontiguous clusters, which are separate and far apart from three clusters of nitrogen fixation genes. Control by quorum-sensing systems has dominated the study of conjugation in the . However, it must be stressed that conjugative transfer may be modulated by other environmental cues, such as nutritional factors.

Citation: Romero D, Brom S. 2004. The Symbiotic Plasmids of the , p 271-290. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch12
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Image of Figure 1
Figure 1

Maps of sequenced pSyms and symbiotic islands. Note that the scale is different between the maps. Abbreviations are defined in the text. Numbers on each map indicate the scale (in kb). References used for each map are as follows: pSymA ( and http://sequence.toulouse.inra.fr/meliloti.html); pNGR234a ( and http://genome.imb-jena.de/other/cfreiber/ pNGR234a2.html); symbiotic island R7A ( and http://sequence.toulouse.inra.fr/msi); symbiotic island MAFF303099 ( and http://www.kazusa.or.jp/rhizobase/). To facilitate comparisons between the symbiotic islands, orientation of the symbiotic island MAFF303099 was reversed from the orientation that appears in the corresponding reference.

Citation: Romero D, Brom S. 2004. The Symbiotic Plasmids of the , p 271-290. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch12
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Image of Figure 2
Figure 2

Schematic organization of systems. Direction of transcription is indicated by arrows. The promoter of the operon is marked with an arrowhead labeled P. The positions of the possible centromere-like sequence αand replication origin βin rhizobial systems are indicated by boxes of different shadings. Possible boxes are shown as a stippled box. Proposed regulatory interactions are also indicated; +, activation; − repression.

Citation: Romero D, Brom S. 2004. The Symbiotic Plasmids of the , p 271-290. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch12
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Image of Figure 3
Figure 3

Comparison of regions involved in conjugal transfer of pSyms and symbiotic islands. (A) Possible regions providing the Dtr functions in rhizobial systems, compared to the corresponding region in pTiC58. Direction of transcription for each gene is indicated by arrows. Empty boxes mark the location of or/T-like sequences. (B) Possible regions providing the Mpf functions in rhizobial systems, compared to the corresponding region in pTiC58. Symbols are as in (A). Interrupted lines connecting two maps mark genes that are absent. See text for details. References for each region are as follows: pTiC58 (25); pNGR234a ( and http://genome.imb-jena.de/other/cfreiber/pNGR234a2.html); symbiotic island R7A ( and http://sequencc.toulouse.inra.fr/msi); symbiotic island MAFF303099 ( and http://www.kazusa.or.jp/ rhizobase/); pSymA ( and http://sequence.toulouse.inra.fr/meliloti. html); pMLb ( and http://www.kazusa.or.jp/ rhizobase/).

Citation: Romero D, Brom S. 2004. The Symbiotic Plasmids of the , p 271-290. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch12
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Figure 4

Location and orientation of identical repeats in sequenced pSyms and symbiotic islands. The sequence of the corresponding pSyms or islands was analyzed using the program Miropeats (86) (available at http://www.jparsons.uklinux.net/bioinf/) running in the intramolecular repeats mode at two different thresholds (300 bp and 1,000 bp, as indicated). All the maps were oriented with the start of the sequence on the left side of the page. Identical repeats are joined by arcs of variable height (lower for direct repeats, higher for inverse repeats). GenBank accession numbers for the sequences analyzed are: pSymA, NC003037; pNGR234a, NC000914; symbiotic island R7A, AL672111. For the symbiotic island MAFF303099, a subfile containing only the sequence of the island was generated from the chromosomal sequence (NC002678); orientation of the subfile was reversed to facilitate comparison with the symbiotic island R7A. Large-scale graphics and analysis tables are available upon request.

Citation: Romero D, Brom S. 2004. The Symbiotic Plasmids of the , p 271-290. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch12
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Generic image for table
Table 1

Distribution of symbiotic plasmids (pSyms) in the family

Citation: Romero D, Brom S. 2004. The Symbiotic Plasmids of the , p 271-290. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch12
Generic image for table
Table 2

replicons in the family

Citation: Romero D, Brom S. 2004. The Symbiotic Plasmids of the , p 271-290. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch12

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