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Plant Physiology 144:615-622 (2007) © 2007 American Society of Plant Biologists Genomes of the Symbiotic Nitrogen-Fixing Bacteria of Legumes1Department of Biology, Center for Environmental Genomics, McMaster University, Hamilton, Ontario, Canada L8S 4K1 (A.M.M., T.M.F.); and Department of Soil, Water, and Climate, BioTechnology Institute and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota 55108 (M.J.S.)
Over the last several decades, there have been a large number of studies done on the genetics, biochemistry, physiology, ecology, and agronomics of the bacteria forming nitrogen-fixing symbioses with legumes. These bacteria, collectively referred to as the rhizobia, are taxonomically and physiologically diverse members of the
The recent completion of the genomes of R. leguminosarum bv viciae (Young et al., 2006
It is now apparent that multipartite genomes are typical among members of -proteobacteria (Jumas-Bilak et al., 1998 -proteobacteria may enhance the bacterium's metabolic or symbiotic capabilities, thus ensuring stable maintenance of the replicon within the population.
Genome size is influenced by environmental factors, and soil-dwelling species, such as the rhizobia, tend to have larger genomes (Bentley and Parkhill, 2004
Symbiotically relevant genes in rhizobia are often clustered on large plasmids (pSym), or within genomic islands (referred to as symbiosis islands [SIs]), emphasizing the accessory nature of the genes and their ability to be acquired via horizontal gene transfer. A SI present in M. loti strain ICMP3153 was found capable of transforming nonsymbiotic strains of M. loti into symbiotic counterparts (Sullivan and Ronson, 1998
Rhizobial genomes appear to be highly dynamic entities and this is particularly reflected by the presence of many insertion sequence (IS) elements, transposases, and related genes, within regions encoding symbiotic functions. The SIs of M. loti and B. japonicum encode the majority of transposase genes and IS-related sequences in these genomes (Kaneko et al., 2000
Palacios and colleagues have performed elegant studies of genome plasticity in rhizobia, demonstrating that extensive recombination occurs within the symbiotic plasmid of Sinorhizobium sp. NGR234 (Flores et al., 2000
The multiphasic lifestyle adopted by rhizobia has influenced the size, complexity, and also the content of their genomes (Bentley and Parkhill, 2004
Rhizobial genomes are richly endowed with transport, regulatory, and stress-related systems, all of which are essential for interacting with the external environment and were acquired subsequent to the divergence of plant-associated Rhizobiales from related
In addition to the rhizobia discussed above, genome sequencing projects have also been initiated or completed for a number of plant-associated
Since nodulation and nitrogen fixation genes in many rhizobia are plasmid borne, the sequences of several large rhizobial plasmids were determined prior to the completion of the whole genome scale projects. The first such initiative involved the complete sequencing of the symbiotic plasmid pNGR234a (Freiberg et al., 1997
Many rhizobial strains appear to carry one or more nonsymbiotic, accessory plasmids that may confer benefits with regard to overall fitness. One such plasmid, the 144 kb pSmeSM11a from S. meliloti, has been sequenced (Stiens et al., 2006
The transcriptome for S. meliloti has been examined under a variety of conditions, including in planta (Ampe et al., 2003
One of the difficulties inherent in working with plant hosts with indeterminate root nodules (such as M. truncatula and alfalfa [Medicago sativa]) is that colonizing bacteria (and plant cells) may be present at various developmental stages. Such a heterogeneous population makes the identification of genes relevant to a particular stage of symbiosis challenging, and may result in apparent discrepancies between different studies (Barnett et al., 2004
Transcriptomics and functional analyses in other rhizobial species are less developed, although micro- and macroarray studies have been performed in B. japonicum and M. loti, respectively. In B. japonicum, an array was used to identify potential members of the NifA and RegR regulons using probes sets specific for >700 candidate genes (Hauser et al., 2006
Genome-wide macroarray experiments performed upon bacteroids from M. loti strain MAFF303099 resulted in the identification of expression islands scattered across the symbiotic island (Uchiumi et al., 2004
While the compilation of genome sequence data represents a significant milestone in the characterization of a bacterial species, assigning gene function to open reading frames (ORFs) is essential to extract information encoded within the nucleotide sequences. One method of addressing this issue is through the construction of an ORFeome, as has been reported in S. meliloti. Schroeder et al. (2005)
The conditions in which genes are expressed may offer valuable insight into the function of the encoded products. For that reason, Cowie et al. (2006)
Systematic gene mutagenesis offers another means of determining gene function via loss of function. Luo et al. (2005)
Several proteomic analyses have now provided additional insight into the symbiosis between S. meliloti and B. japonicum and their host legumes (Natera et al., 2000
The transcriptomes and proteomes of bacteroids differ considerably from those of free-living cells (Perret et al., 1999
The actinomycete Frankia forms nitrogen-fixing root nodules on nonlegumes and the genetic basis of the symbiotic interactions between Frankia strains and host plants is poorly understood. Accordingly, the recent publication of genomic sequences of three Frankia sp. strains is an exciting development (Normand et al., 2007
Traditionally, studies involving rhizobia have focused upon a subset of genes involved in root nodulation, nitrogen fixation, and other symbiotic processes. However, the recent completion of genome sequencing projects in several rhizobial species permits a more comprehensive analysis of gene function and evolution. One trend that has emerged is the highly dynamic and complex nature of rhizobial genomes. As well, it is becoming increasingly evident that genome architecture and even content is significantly influenced by the multiphasic lifestyle adopted by legume endosymbionts.
Transcriptomic and proteomic analyses have provided valuable insight into rhizobial-legume symbioses, however, significant limitations still exist within these types of studies. This is perhaps best exemplified in studies involving indeterminate root nodules, where the issue of analyzing expression patterns at various stages of infection has been addressed through the use of bacterial and plant developmental mutants. The poor overlap that has been documented between transcriptomic and proteomic data emphasizes the importance of developing additional functional genomic approaches, such as studies focusing upon the metabolomics of stem- and root-nodule bacteria (Barsch et al., 2004
We thank Eddie Cytryn for help with the construction of the phylogenetic tree of 16S rDNA sequences. Received April 26, 2007; accepted May 3, 2007; published June 6, 2007.
1 This work was supported by grants from the Natural Sciences and Engineering Research Council of Canada, Genome Canada, and the Ontario Research and Development Challenge Fund (to A.M.M. and T.M.F.), and from the University of Minnesota Agricultural Experiment Station and U.S. Department of Agriculture/Cooperative State Research, Education, and Extension Service/National Research Initiative (grant no. 20043560414708 to M.J.S.). The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Turlough Finan (finan{at}mcmaster.ca). www.plantphysiol.org/cgi/doi/10.1104/pp.107.101634 * Corresponding author; e-mail finan{at}mcmaster.ca; fax 9055226066.
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