the genetics of symbiotic nitrogen fixation: comparative ...€¦ · genes 2012 3 143 2.1.3....
TRANSCRIPT
�
Genes 2012, 3, 138-166; doi:10.3390/genes3010138
genesISSN 2073-4425
www.mdpi.com/journal/genes Article
The Genetics of Symbiotic Nitrogen Fixation:Comparative Genomics of 14 Rhizobia Strains byResolution of Protein Clusters
Michael Black 1,*, Paula Moolhuijzen 1, Brett Chapman 1, Roberto Barrero 1, John Howieson 2,Mariangela Hungria 3 and Matthew Bellgard 1,*
1 Centre for Comparative Genomics, Murdoch University, South Street, Murdoch, Perth, WA 6150, Australia; E-Mails: [email protected] (P.M.); [email protected] (B.C.); [email protected] (R.B.);
2 Centre for Rhizobium Studies, Murdoch University, South Street, Murdoch, Perth, WA 6150, Australia; E-Mail: [email protected]
3 Embrapa Soja, Cx. Postal 231, Londrina, Parana, 86001-970, Brazil; E-Mail: [email protected]
* Author to whom correspondence should be addressed; E-Mails: [email protected]; [email protected].
Received: 24 January 2012; in revised form: 10 February 2012 / Accepted: 13 February 2012 / Published: 16 February 2012
Abstract: The symbiotic relationship between legumes and nitrogen fixing bacteria is critical for agriculture, as it may have profound impacts on lowering costs for farmers, on land sustainability, on soil quality, and on mitigation of greenhouse gas emissions. However, despite the importance of the symbioses to the global nitrogen cycling balance, very few rhizobial genomes have been sequenced so far, although there are some ongoing efforts in sequencing elite strains. In this study, the genomes of fourteen selected strains of the order Rhizobiales, all previously fully sequenced and annotated, were compared to assess differences between the strains and to investigate the feasibility of defining a core ‘symbiome’—the essential genes required by all rhizobia for nodulation and nitrogen fixation. Comparison of these whole genomes has revealed valuable information, such as several events of lateral gene transfer, particularly in the symbiotic plasmids and genomic islands that have contributed to a better understanding of the evolution of contrasting symbioses. Unique genes were also identified, as well as omissions of symbiotic genes that were expected to be found. Protein comparisons have also allowed the identification of a
OPEN ACCESS
Genes 2012, 3
139
variety of similarities and differences in several groups of genes, including those involved in nodulation, nitrogen fixation, production of exopolysaccharides, Type I to Type VI secretion systems, among others, and identifying some key genes that could be related to host specificity and/or a better saprophytic ability. However, while several significant differences in the type and number of proteins were observed, the evidence presented suggests no simple core symbiome exists. A more abstract systems biology concept of nitrogen fixing symbiosis may be required. The results have also highlighted that comparative genomics represents a valuable tool for capturing specificities and generalities of each genome.
Keywords: nitrogen fixation; symbiosis; Rhizobiales; genome; comparative genomics; nodulation genes; secretion systems
1. Introduction
The symbiotic relationship between legumes and nitrogen fixing bacteria is critical for agriculture, as it may have profound impacts on lowering costs for farmers, on land sustainability, on soil quality, and on mitigation of greenhouse gas emissions. The major importance of the symbioses is usually attributed to the decrease in the use of costly nitrogen based fertilizers, but the rehabilitation of infertile, environmentally stressed soils should also be highlighted. With an increasing global demand for food production, combined with the need to reduce carbon emissions, the reliance on biological nitrogen fixation as an alternative to nitrogen fertilizers is forecast to increase [1].
Symbiotic nitrogen fixing bacteria are represented by a phylogenetically disparate class of alpha- and beta-proteobacteria—usually collectively termed rhizobia—that have achieved the function of fixing atmospheric nitrogen (N2) in symbiosis with legumes. The majority of the symbiotic speciesare represented in the alpha-proteobacteria order Rhizobiales, which, amongst many others, contain the agriculturally important nitrogen fixing genera of Rhizobium, Bradyrhizobium, Mesorhizobium, Sinorhizobium (=Ensifer) and Azorhizobium. One impediment to the broader use of rhizobia in agriculture is the production of compatible inoculants. There are substantial host, strain and environmental specificities that limit the use of potentially important legume fodder and crops as alternatives to nitrogen fertilizers [2,3].
Despite the importance of nitrogen fixation to the global nitrogen balance, very few rhizobial strains have been completely sequenced, representing less than 1% of the complete bacterial genomes available today. The scenario may slightly improve in the following years, as there are large-scale genome sequencing projects in progress. Furthermore, very few genomic studies comparing nitrogen fixing bacteria have been performed [4,5], but the results obtained have indicated that comparative genomics represents a promising tool to reveal bacterial specificities. Furthermore, advances in bioinformatics tools will reveal increasing details in the comparison of genomes.
In this present study, fourteen rhizobial genomes were selected based on maximizing geographical, environmental and host range, spanning most Vavilov centers of origin [6]. This comparison was undertaken to attempt to establish a reference ‘symbiome’, meaning a set of genes critical to successful
Genes 2012, 3
140
symbiosis and subsequent nitrogen fixation, as well as to obtain a better understanding of the strategies adopted by disparate strains to maintain their symbiotic apparatus. Different tools were evaluated in the comparison, and the results may also contribute to a further exploration in future large scale comparative genomic studies.
2. Results and Discussion
2.1. Key Characteristics of the Fourteen Strains of the Order Rhizobiales
The aim of this study was to investigate the possibility of defining a common ‘symbiome’ amongst selected nitrogen fixing strains of the order Rhizobiales. The fourteen genomes selected represent a broad range, from classic legume symbionts to Mesorhizobium sp. BNC1, a strain that has seemingly lost the ability to fix nitrogen and form symbiotic relationships. In addition, the selected organisms represent both root nodulating (e.g., Bradyrhizobium japonicum USDA 110, symbiont of soybean—Glycine max, Sinorhizobium meliloti 1021, symbiont of alfalfa—Medicago sativa)) and stem nodulating (e.g., Azorhizobium caulinodans strain ORS571, symbiont of sesbania—Sesbania rostrata) microsymbionts. All available nucleotide and protein FASTA files, as well as GENBANK files available were utilized (Table 1). The fourteen genomes sequenced and their hosts are listed in Table 2, and the strains will be referred to by their KEGG organism code.
2.1.1. Azorhizobium
A. caulinodans (azc) is a nitrogen fixing member of the Xanthobacteraceae family. It is primarily a stem nodulator of the African legume sesbania. It is thought to have originally been a non-nitrogen fixer that developed the ability to fix N2 entirely through lateral gene transfer from another unknown species [7]. Unlike the other thirteen strains from this study, azc can reduce di-nitrogen both in symbiosis and in the free living stage, and as a result can be grown on nitrogen free medium, a key defining property. It has a relatively small genome—5.37 MB—in comparison to other rhizobia and it is the most taxonomically distant species in this study [7,8].
2.1.2. Bradyrhizobium
Three Bradyrhizobium genomes have been selected, B. japonicum USDA 110 (bja), Bradyrhizobium sp. BTAi1 (bbt), and Bradyrhizobium ORS278 (bra). Bradyrhizobium is primarily distinguished from the genera Mesorhizobium, Rhizobium and Sinorhizobium by the slower growth rate (doubling time) of at least 8 h.
The soybean root nodulator bja has the largest genome of this study, 9.1 MB, in a unique chromosome [9]. The main feature of the more recently obtained genomes of Bradyrhizobium strains BTAi1 (bbt) and ORS278 (bra) is that they are photosynthetic stem nodulators of tropical Aeschynomene species, and for the first time described as lacking common nodulation genes nodA, nodB and nodC. These genes are traditionally involved in the construction of the Nod factor backbone [10,11]. Both strains also have large genomes, similar to bja (Table 2).
Genes 2012 3�
�
141
Table 1. REFSEQ identifiers for the fourteen Rhizobiales genomes.
Rhizobium species Chr Plasmid1 Plasmid2 Plasmid3 Plasmid4 Plasmid5 Plasmid6 Azorhizobium caulinodans ORS 571 NC_009937 - - - - - - Bradyrhizobium japonicum USDA 110 NC_004463 - - - - - - Bradyrhizobium sp. BTAi1 NC_009485 NC_009475 Bradyrhizobium sp. ORS 278 NC_009445 - - - - - - Mesorhizobium loti MAFF303099 NC_002678 NC_002679 NC_002682 Mesorhizobium sp. BNC1 (Chelativorans sp. BNC1) NC_008254 NC_008242 NC_008243 NC_008244 Rhizobium etli CFN 42 NC_007761 NC_007762 NC_007763 NC_007764 NC_004041 NC_007765 NC_007766 Rhizobium etli CIAT 652 NC_010994 NC_010998 NC_010996 NC_010997 Rhizobium leguminosarum bv. trifolii WSM1325 NC_012850 NC_012848 NC_012858 NC_012853 NC_012852 NC_012854 Rhizobium leguminosarum bv. trifolii WSM2304 NC_011369 NC_011368 NC_011366 NC_011370 NC_011371 Rhizobium leguminosarum bv. viciae 3841 NC_008380 NC_008382 NC_008383 NC_008379 NC_008381 NC_008384 NC_008378 Sinorhizobium fredii sp. NGR 234 NC_012587 NC_000914 NC_012586 Sinorhizobium medicae WSM419 NC_009636 NC_009620 NC_009621 NC_009622 Sinorhizobium meliloti 1021 NC_003047 NC_003037 NC_003078
Table 2. Summary statistics of the fourteen genomes of Rhizobiales.
Rhizobiales speciesSpeciesCode
No. of Plasmids
Total GenomeLength
(nucleotides)
Protein CodingGenes
tRNA genes
Pseudo genes
GCContent
(%)
Proportion of Genome that
is Gene Coding (%)
Host (Scientific/common name)
Azorhizobium caulinodans ORS 571 azc 0 5,369,772 4717 63 - 67 89 Sesbania rostrata (sesbania) Bradyrhizobium japonicum USDA 110
bja 0 9,105,828 8317 56 - 64 86 Glycine max (soybean)
Bradyrhizobium sp. BTAi1 bbt 1 8,493,513 7621 70 90 64 85 Aeschynomene indica (Indian joint-vetch)
Bradyrhizobium sp. ORS 278 bra 0 7,456,587 6717 66 35 65 85 Aeschynomene sensitiva (sensitive joint-vetch)
Genes 2012, 3
142
Table 2. Cont.
Rhizobiales speciesSpeciesCode
No. of Plasmids
Total GenomeLength
(nucleotides)
Protein CodingGenes
tRNA genes
Pseudo genes
GCContent
(%)
Proportion of Genome that
is Gene Coding (%)
Host (Scientific/common name)
Mesorhizobium loti MAFF303099 mlo 2 7,596,297 7272 57 - 62 86 Lotus sp.,including Lotus japonicas (trifoils, vetches)
Mesorhizobium sp. BNC1 mes 3 4,935,185 4543 68 40 61 89 non-symbiotic Rhizobium etli CFN 42 ret 6 6,530,228 5963 59 32 61 86 Phaseolus vulgaris (common bean) Rhizobium etli CIAT 652 rec 3 6,448,048 6056 60 15 61 86 Phaseolus vulgaris (common bean)
Rhizobium leguminosarum bv. trifolii WSM1325
rlg 5 7,418,122 7001 63 75 61 86 Trifolli pratense and other Mediterraneum Trifollium (clovers),
Rhizobium leguminosarum bv.trifolii WSM2304
rlt 4 6,872,702 6415 65 45 61 86 Trifolium polymorphum from Uruguay (clover)
Rhizobium leguminosarum bv. viciae 3841
rle 6 7,751,309 7143 61 37 61 86 Tribe Viciae –Vicia, Pisum, Lathyrus, Lens (vetchs, peas, lathyrus, lentils)
Sinorhizobium fredii NGR 234 rhi 2 6,891,900 6363 70 - 63 87 112 legume species and the non-legume Parasponia (family Ulmaceae)
Sinorhizobium medicae WSM419 smd 3 6,817,576 6213 63 43 61 87 Medicago spp.
Sinorhizobium meliloti 1021 sme 2 6,691,694 6218 66 4 62 86 Medicago,Melilotus, Trigonella (alfalfa)
Genes 2012 3�
�
143
2.1.3. Mesorhizobium
As the suffix Meso suggests, species of this genus show growth rates intermediate to Bradyrhizobium (>8 h) and Rhizobium/Sinorhizobium (<6 h). Mesorhizobium loti MAFF303099 (mlo) is a root nodulator of Lotus japonicum, with one chromosome and two plasmids; as in other Mesorhizobiumand Bradyrhizobium, mlo has a symbiotic island within the chromosome that contains all key genes for nodulation and nitrogen fixation [12].
Mesorhizobium sp. BNC1 (mes), formerly known as Agrobacterium sp. BNC1, and alternately named Chelativorans sp. BNC1, is the functional outlier of the fourteen species, being asymbiotic. It was isolated from a mixed-culture enriched from sewage using the chelating agent EDTA as the sole carbon and nitrogen source [13]. For this study, mes is utilized as an outlier for the basis of “symbiome” definition and investigation.
2.1.4. Rhizobium
The genus Rhizobium, originally defining all bacterium with the ability to nodulate legumes [14], has undergone multiple redefinitions and now encompasses a variety of fast growing nitrogen fixers including some former Agrobacterium and Sinorhizobium (Ensifer) species and the genus Allorhizobium. In this study, five Rhizobium genomes are investigated: R. etli CFN 42 (ret), R. etli CIAT 652 (rec), R.leguminosarum bv. trifolii WSM1325 (rlg), R. leguminosarum bv. trifolii WSM2304 (rlt) and R. leguminosarum bv. viciae 3841 (rle). These five Rhizobium strains have different origins and hosts. The R. etli strains nodulate common bean (Phaselous vulgaris and were originally isolated in Central America) [15–18]. In contrast, the R. leguminosarum strains nodulate temperate legumes: bv. trifolii rlg and rlt are symbionts of clovers (Trifolium), although individually matched to annual (rlg) and perennial (rlt) species for N fixation [19,20], Bv. viciae rle has a broader host range, nodulating legumes within the tribe Viciae, including Pisum, Vicia, Lathyrus and Lens [21].
2.1.5. Sinorhizobium
The genus Sinorhizobium is subject of some controversy. Members of this genus were originally classified as Rhizobium (e.g., Rhizobium meliloti) and the new genus was proposed in 1988 [22].More recently, the genus has been reclassified as Ensifer [23,24], but in general the new nomenclature was not broadly accepted by rhizobiologists. Sinorhizobium and Rhizobium have similar morpho-physiological properties, and only the 16S rRNA taxonomy resolves the genus as a distinct clade [25].
Three Sinorhizobium were chosen for this study, S. meliloti 1021 (sme), S. medicae WSM419 (smd) and Sinorhizobium sp. strain NGR 234 (rhi), also denominated as S. fredii NGR 234 and Rhizobium sp. NGR 234 [26–28]. Both sme and smd nodulate temperate legumes of the genus Medicago. It has been established that smd has greater acid tolerance, and is a more effective nodulator of Medicagotruncatula than sme [29,30]. It is also hypothesized that sme and smd evolved in association with hosts adapted to different edaphic conditions [31]. The tropical strain NGR 234 (rhi) is probably the most intriguing rhizobia isolated so far. Originally isolated in Papua New Guinea and labeled Rhizobium sp. NGR 234, it has since been found to be highly promiscuous, capable of nodulating at least 112
Genes 2012, 3
144
different legume genera, from most Vavilov centers of origin, in addition to the non-legume Parasponia [32–34].
2.2. Phylogeny and Taxonomy of Rhizobiales
2.2.1. 16S rRNA Taxonomy
The phylogeny and taxonomy of nitrogen fixing Rhizobiales is in a state of flux. Confusion over the status of Sinorhizobium [22,23,35] and the split phylogeny of Agrobacterium within the genus Rhizobium [24,36] are just two cases in point. Therefore in this genomic comparison several methods of taxonomic and genomic comparison were utilized to highlight different aspects of the phylogeny of the selected strains.
Figure 1. 16S rRNA gene tree built with the multiple 16S rRNA genes from each of the fourteen genomes compared. Taxonomic analysis performed with MEGA5 [68], by constructing a bootstrapped neighbor-joining (NJ) gene tree with Jukes-Cantor substitution.
Genes 2012, 3
145
The ‘classical’ relationship between Bradyrhizobium, Rhizobium, Sinorhizobium and Mesorhizobium is clearly shown in the 16S rRNA phylogeny (Figure 1). The four major groups are delineated from each other forming four major clusters, with Azorhizobium as a separate branch. All strains were clustered within the expected genera and as expected the Trifolium nodulators rlg and rlt were indistinguishable from each other using exclusively the 16S rRNA.
2.2.2. Dotplot Analysis
Further comparison of whole chromosomes adds valuable information to the 16S rRNA taxonomy results. A dotplot of the chromosome nucleotide sequences was compiled using an in-house application called FRECKLE (Figure 2) (http://code.google.com/p/freckle/). Two primary blocks of significant sequence similarity are those of the Bradyrhizobium species with another larger block consisting of the Rhizobium and Sinorhizobium strains, while Azorhizobium and Mesorhizobium are outliers. The sme chromosome shows a highly repetitive structure, more than any other chromosome. Interestingly, the dotplot also displayed a strong sequence similarity between Sinorhizobium NGR 234 and S. meliloti 1021, including a shared repetitive structure.
Figure 2. FRECKLE DNA dotplot of the fourteen Rhizobiales chromosomes, constructed from nucleotide FASTA files using an in house script.
A dotplot of plasmids (Figure S1) shows markedly less homology. Greater symmetries were detected in Rhizobium non-symbiotic plasmids: plasmids p42e (R. etli CFN 42), pRL11 (R. leguminosarum bv. viciae 3841), pRLG202 (R. leguminosarum bv. trifolii WSM2304) and
Genes 2012, 3
146
pR132502 (R. leguminosarum bv. trifolii WSM132502) are especially homologous, suggesting higher stability. In addition, pSMED01 (S. medicae WSM419) and pSymB (S. meliloti 1021) also show symmetry. This observation has been previously explored, resulting in the proposal that these plasmids—with little or no direct involvement in the symbiosis—represent secondary chromosomes [37], or alternatively ‘chromids’ [38], as they contain essential metabolic genes, as well as tRNA and/or rRNA.
In contrast, little homology was detected in the analysis of the symbiotic plasmids (Figure S1). Symbiotically important plasmids have similar nod, nif and, in some cases, fix clusters. It is hypothesized that multiple lateral transfer events, which originally enabled the symbiotic and nitrogen fixing ability of many of these bacteria, would have also caused the overall lack of homology amongst the symbiotic plasmids. Our study has pointed out that the rhi plasmids pNGR234a and pNGR234b display lesser homology with the other plasmids, suggesting a greater number of lateral transfer events. Such ‘elastic’ genomes could partly explain the adaptation to a wide host range of rhi.
The contrast between the 16S rRNA taxonomy and the two dotplots (chromosomal and plasmids) relies on the disparate relationships between the plasmids. In fact, Young et al. 2006 concluded that R. leguminosarum bv. viciae (rle) had a core genome, mostly chromosomal with a high G+C content and shared with other organisms, and an accessory genome with a lower G+C content, on plasmids and chromosomal genomic islands [21]. The broader whole genome taxonomy in this study suggests that this two-component genome model may prevail in other rhizobial species. The R. etli and R. leguminosarum bv. trifolii genomes species share much of their chromosome with R. leguminosarum bv. viciae, further expanding the “core—genome” definition of Young et al. 2006, and, in turn, shrinking the “accessory genome”.
Most important, the low homology observed in this study in the comparison of the genomes of both closely related strains within the same species and also between species showing reasonable similarity of the 16S rRNA, and clearly showing several events of lateral gene transfer reinforces the discussion about the validity of prokaryote species definition [39,40].
2.3. KEGG Orthology and Protein Clustering
2.3.1. KEGG Pathway Analysis
The next stage of our genomic study was to compare KEGG genes and pathways in each species. The summary of KEGG orthologs is shown in Table 3, and the full table of KEGG pathways is included as Table S1.
All fourteen genomes have a large number of nitrogen, methane, sulfur, amino acid, vitamins and cofactors metabolism KEGG orthologs. This diverse suite of metabolism pathways is indicative of the ability to live in the complex rhizosphere environments, as well as to adapt to the nodule environment. However, the fact that the non-symbiotic genome of mes shows the same wide range of KEGG metabolism pathway orthologs as the symbiotic mlo, indicates the role of these genes in determining saprophytic capacity in a broad range of soil conditions. Noteworthy was the wide range of nitrogen metabolism protein orthologs detected (Table S2), showing a variety of nitrogen metabolism capabilities. The largest number of orthologs in Bradyrhizobium and Sinorhizobium indicate the
Genes 2012, 3
147
capacity to metabolize nitriles, nitrates, formamide, nitroalkanes, as well as related amino acids glutamine and asparagine.
The genomes of Mesorhizobium and Rhizobium leguminosarum lack norC, norD and norE orthologs, protein subunits of the nitric oxide reductase complex. Interestingly, within the same species R. etli, ret but not rec contains asparagine synthetase (asnB) and nor orthologs. R. etli CFN 42 (ret) is unable to use nitrate for respiration and lacks nitrate reductase activity, as well as the nap and nar genes encoding respiratory nitrate reductase; however, the strain carries proteins closely related to denitrification enzymes, norCBQD. The functionality of nor genes in CFN 42 has been recently demonstrated, allowing the reduction of nitrite and nitric oxide [41]. It is worth mentioning that differences between strains within the same species made visible only by comparative genomics can help to explain metabolomic advantages, e.g., in this case of ret over rec.
2.3.2. Protein Cluster Analysis
A comprehensive method of comparative genome analysis is to cluster protein families with the BlastlineMCL algorithm [42], representing a Markov clustering of all orthologous protein groups across species. This could be considered a more complete clustering of orthologous proteins than from KEGG, as it includes all proteins annotated across all the genomes, not just the more restricted set of established KEGG orthologs. The use of this tool has been shown to be crucial in the comparison of rhizobial species, as many symbiotic and nitrogen fixing related gene pathways and families are not represented in KEGG.
Cluster information resolved from BlastlineMCL analysis is available online (see experimental section), where users can compare any combination of genome protein family homology to search for orthologous protein groups of interest. Raw sequence data is available in FASTA format and CLUSTALW aligned format (MSF). This resource represents a vast repository of comparative genomics information on the fourteen genomes, of which only a few are discussed in this paper.
A nitrogen-fixing Rhizobiales “pan-genome” of 1,126 clusters and 28,110 proteins was resolved amongst the fourteen genomes (Table 4). The clusters within this group include ABC transporters, some transposases, ribosomal RNA synthetases, DNA polymerases and other core proteins. The ABC transporters are the second most abundant family of non-hypothetical protein encoding genes found in all sequenced prokaryotic, eukaryotic, viral genomes as well as in metagenomic sequences. ABC transporters represent one of the largest superfamilies of active membrane transport proteins (MTPs), with a highly conserved ATPase domain that binds and hydrolyzes ATP, supplying energy for the uptake of a variety of nutrients and for the extrusion of drugs and metabolic wastes [43]. It is therefore not surprising that by far the biggest cluster found in the BlastlineMCL analysis is that of ABC type transporters, with 1,128 separate proteins. Together with the previous KEGG findings, this is indicative of ability to use a very wide range of substrates, a key property for adaption in the variety of environments, such as the numerous geographical rhizospheres represented (such as China, Papua New Guinea, Uruguay and Mexico) and the diverse hosts they nodulate.
Genes 2012 3�
�
148
Table 3. Summary of KEGG pathway and protein orthologs in the fourteen Rhizobiales genomes.
Relevant KEGG Pathways Number of KEGG Protein Orthologs
azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme 1.1 Carbohydrate Metabolism 240 295 295 296 274 245 249 279 257 256 299 262 267 273 1.2 Energy Metabolism 114 147 146 145 113 114 112 111 99 99 118 111 124 138 1.3 Lipid Metabolism 52 63 72 72 72 53 61 76 58 57 81 56 58 71 1.4 Nucleotide Metabolism 102 96 100 99 111 105 100 108 97 99 112 97 98 114 1.5 Amino Acid Metabolism 221 249 268 258 275 224 235 261 227 241 272 239 236 253 1.6 Metabolism of Other Amino Acids 50 58 62 57 60 48 54 58 54 57 58 56 54 62 1.7 Glycan Biosynthesis and Metabolism 30 29 31 33 32 25 33 35 32 34 36 31 22 32 1.8 Metabolism of Cofactors and Vitamins 117 132 143 137 131 103 122 126 114 117 130 119 117 124 1.9 Biosynthesis of Polyketides and Terpenoids 29 29 42 43 29 27 28 36 28 27 34 27 27 34 1.10 Biosynthesis of Other Secondary Metabolites 8 21 32 35 31 20 27 34 26 26 37 26 23 28 1.11 Xenobiotics Biodegradation and Metabolism 85 134 166 163 97 72 58 129 60 59 138 55 53 101 2.1 Transcription 4 4 4 4 4 4 4 4 4 4 4 4 4 4 2.2 Translation 134 131 128 129 130 123 128 128 129 129 127 124 129 132 2.3 Folding, Sorting and Degradation 40 40 38 38 36 34 36 37 38 38 37 36 38 38 2.4 Replication and Repair 69 74 71 71 70 70 71 71 73 71 73 70 71 71 3.1 Membrane Transport 119 141 121 114 172 135 159 163 138 131 162 165 148 170 3.2 Signal Transduction 57 61 55 57 50 39 50 55 48 48 53 49 46 49 4.2 Cell Motility 38 41 43 43 34 38 40 41 40 40 41 40 40 40 Total KEGG Protein Orthologs 1509 1745 1817 1794 1721 1479 1567 1752 1522 1533 1812 1567 1555 1734
Table 4. Summary of selected MCL BLASTline protein cluster groups.
Cluster Family Clusters Proteins Proteins in
Chromosomes Proteins in Plasmids
Percent in Chromosomes
Percent in Plasmids
Pan-genome (all 14) 1126 28110 23686 4424 84.26 15.74 13 Fix+ genomes 105 1126 619 507 54.97 45.03 11 NodABC+ genomes 9 113 60 53 53.10 46.90
Genes 2012, 3
149
Table 4. Cont.
Cluster Family Clusters Proteins Proteins in
Chromosomes Proteins in Plasmids
Percent in Chromosomes
Percent in Plasmids
azc+bbt+bja+bra 206 1150 1141 9 99.22 0.78 bbt+bja+bra 857 2981 2976 5 99.83 0.17 bbt+bra 577 1224 1224 0 100.00 0.00 mlo+mes 86 192 167 25 86.98 13.02 mes+mlo+rhi+ret+rec+rlg+rlt+rle+smd+sme 214 2424 2081 343 85.85 14.15 mlo+rhi+ret+rec+rlg+rlt+rle+smd+sme 161 1661 1140 521 68.63 31.37 rhi+ret+rec+rlg+rlt+rle+smd+sme 155 1347 1122 225 83.30 16.70 rhi+ret+rec+rlg+rlt+rle 51 347 191 156 55.04 44.96 rlg+rlt+rle 92 286 197 89 68.88 31.12 smd+sme 253 555 182 373 32.79 67.21 rhi+ret+rec 6 21 5 16 23.81 76.19 rhi+smd+sme 242 767 476 291 62.06 37.94 ret+rec 123 262 71 191 27.10 72.90 ret+rec+rlg+rlt+rle 352 1866 1436 430 76.96 23.04 Singletons azc 956 986 986 0 100.00 0.00 bja 1760 1839 1839 0 100.00 0.00 bbt 1051 1107 1005 102 90.79 9.21 bra 959 987 987 0 100.00 0.00 mlo 1706 1809 1613 196 89.17 10.83 mes 857 899 761 138 84.65 15.35 ret 333 344 196 148 56.98 43.02 rec 563 563 374 189 66.43 33.57 rlg 576 602 260 342 43.19 56.81 rlt 490 492 286 206 58.13 41.87 rle 542 550 276 274 50.18 49.82 rhi 758 797 356 441 44.67 55.33 smd 598 639 317 322 49.61 50.39 sme 472 498 170 328 34.14 65.86
Genes 2012 3
150
The number of clusters shared amongst all thirteen nitrogen fixers was of 105, containing a total of 2,038 proteins. Many of these clusters are of nif proteins, the components of the nitrogenase complex. Nine protein clusters were shared by the eleven strains containing the nodABC genes, with a total of 113 proteins. These clusters include other nod, nol and noe gene families, protein families crucial to nodulation.
Table 4 lists many other cluster sharing combinations. For example, 857 clusters are exclusively shared by the Bradyrhizobium species, confirming the differences between this genus and the others. In addition, the 242 clusters containing 767 proteins—60% in chromosomes—found only in rhi, smd, sme confirm rhi as a Sinorhizobium species.
The number of singleton clusters (clusters containing proteins only from one species) approximately correlated with previously resolved taxonomic divisions, as well as genome size (Table 4). The largest number of singletons was found in the biggest genome, bja (1,760 clusters containing 1,839 proteins). The number of singletons amongst the various Rhizobium and Sinorhizobium was much smaller, ranging from 758 clusters containing 797 proteins in rhi to 333 clusters containing 344 proteins in rec. The most common protein family found amongst these singletons is composed by hypothetical proteins.
2.4. The “Symbiome”- Nodulation, Secretion, Exopolysaccharide Production, Oxygen Transport and Nitrogen Fixation
A precise definition of what is included in a theoretical ‘symbiome’ is still elusive. For the purposes of the current study, the core ‘symbiome’ is defined as the protein families, found in the BlastlineMCL clusters, involved in symbiosis and in nitrogen fixation. For this study this is defined as proteins for nodulation, secretion, exopolyssacharide production, oxygen transport and nitrogen fixation. The concept of a “symbiome’ spans plasmids, genetic islands, as well as the rest of the chromosome. It is loosely based on the concept of ‘core’ and ‘accessory’ genomes, where the ‘accessory’ genome has a lower GC content and usually, but not always, is composed of plasmids and/or genomic islands [21].
In general, nodulation gene clusters have been found in close proximity to nif and fix genes. In rhizobial species carrying plasmids, nodulation (nod, nol and noe), nif and fix, as well as many secretion related genes, are found in a symbiotic plasmid, while in species or strains without plasmids, the genes are located in laterally transferrable genomic islands, also denominated as symbiotic islands. For example, in R. leguminosarum bv. viciae 3841 most symbiotic genes are located in plasmid pRL10 [21], while in mlo a 500 kb genomic island carries the genes responsible for symbiosis [11,44]. However, there are exceptions, e.g., Sinorhizobium NGR 234, in which nif and nod operons are located on a plasmid, while the fix genes are on the chromosome [34]. Also in R. etli CFN 42, the pSym p42d contains most of the genes needed for symbiosis, but homologs for nodulation genes are found in other replicons of the genome [16]. These symbiotic regions of nitrogen fixing Rhizobiales genomes have been found to be largely mosaic structures that have been frequently tailored by recombination, horizontal transfer and transposition [15].
In the thirteen symbiotic nitrogen fixing bacterial genomes compared, there is a range of symbiosis region arrangements. The simplest is in azc, which contains a small 87.1 kb symbiotic island with nodand trb operons responsible for the production of Nod factor and type IV secretion, respectively [7]. The nif and fix gene families are in separate regions of the chromosome. As azc is unique amongst the
Genes 2012 3
151
fourteen genomes in being able to fix nitrogen without symbiosis, it has been hypothesised that this symbiotic island has been laterally transferred to azc some time after its initial evolution [7].
Both bja and mlo possess large symbiotic islands (~500 kb) containing all nodulation, nif and fix genes as well as some secretion related genes [9,44]. The other ten symbiotic nitrogen fixers all have symbiotic plasmids in which most of the nodulation, nif, fix and secretion genes are located [16,17,21,26,28,45].
2.4.1. Nod Genes
Induction of nodulation genes leads to the production and secretion of return signals, the Nod Factors, which are lipochitooligosaccharides of variable structure. Nod factors are essential for the Rhizobiales to trigger root hair curling, to induce the formation of nodule primordia, and to enter the root via infection threads. Purified Nod factors are sufficient to induce root hair deformations, cortical cell divisions, and on some host plants, fully grown nodule-like structures. NodD is the core signaling protein, reacting to plant flavonoids then binding to nod boxes, binding sites upstream of nod genes, typically nodA and/or nodB, triggering the expression of a nod gene cascade and thus the construction of the Nod Factor (e.g., [46]).
The results of BlastlineMCL clustering were utilized to the extraction of all nod protein ortholog clusters (Table S3). In total, twenty five different Nod protein ortholog clusters amongst the fourteen species were found. All fourteen species contained nodD, nodE, nodG, nodI, nodM, nodP, nodQ, nodV and nodW. Unsurprisingly, the non-symbiotic mes had the least number of nod genes, with ten. In a previous study, nodD and nodM have also been indicated as common genes of bacteria of the order Rhizobiales, but including both symbiotic and pathogenic stains [5].
One of the Nod orthologs found in all species is NodG, which is in the second largest MCL cluster. It is a cation protein exporter, involved in the secretion of the finished Nod factor into the environment. It is noteworthy that in R. tropici strain PRF 81 nodG can be promptly transcribed—after only 5 min—in the presence of host specific flavonoids [47].
Two nod genes were found exclusively in one strain: nodR in R. leguminosarum bv. trifoliiWSM1325 and nodO in R. leguminosarum bv. viciae 3804. The function of nodR is unknown; however, it is suspected that NodR might contribute to the superior host nodulation efficiency of WSM1325, compared to WSM2304 [20]. In relation to NodO, it catalyzes the addition of carbamoyl to the Nod factor backbone [48], and it is also a calcium-binding protein that promotes infection thread development in root hairs [49]. Interestingly, in Rhizobium sp. BR 816 (reclassified as Sinorhizobium) the transfer of nodO can extend its host range [50], therefore it might be involved in the ability of rle to nodulate a wide range of species within the Viciae tribe.
While all species have many core and non-core nod genes, an investigation of nod operon/gene structure in the thirteen symbiotic genomes displays a wide variety of arrangements. The Sesbania nodulator azc has a large nod operon nodABCSUIJZnoeCHOP with nodD1 located downstream [7]. The soybean nodulator bja also has a large nod operon nodD1-YABCSUIJ [9]. Surprisingly, the other two Bradyrhizobium, bbt and bra, have no nodA, nodB or nodC genes [11], and the signaling mechanisms with the host plant are still under investigation [10].
The three R. leguminosarum and the two Sinorhizobium genomes studied have similar initial nod operon structures, nodDABCIJ. In R etli, the arrangement differs with nodD, nodIJ, a 200 bp gap and
Genes 2012 3
152
then nodCB; the gene nodA is 16 kb downstream. Finally, in mlo, there is a separate nodAC and nodIJoperon, with nodD and nodB in disparate regions of the 600 kb symbiotic island.
Figure 3. Phylogeny of NodD proteins of the Rhizobiales genomes from this study, achieved through a neighbor joining (NJ) gene tree based on BLOSUM-62 matrix alignment of the proteins in the NodD cluster. Number in sequence label is the GENBANK protein GI number. Colored line indicates genus of each genome as coded for in Tables S1 to S18, as well as that the protein is a confirmed NodD protein. Black lines indicate protein is only a putative protein within the LysR family.
Genes 2012 3
153
The most intriguing organization is found in rhi, apparently a composite arrangement. It has a nodABC operon, a gap of 152 bp, following a nodIJ operon. nodD1 is ~200 kb downstream from nodAB [34]. This arrangement of key nod genes in rhi seems to be a composite of R etli, R.leguminosarum and Sinorhizobium nod gene arrangements.
The taxonomy of nod genes of the fourteen genomes was further explored by measuring the similarity of the NodD proteins within the designated MCL cluster. This was achieved through a neighbor joining (NJ) gene tree based on BLOSUM-62 matrix alignment of the proteins in that cluster (Figure 3). The cluster itself is a broad collection of LysR transcription regulator-like proteins, and it is divided onto two broad branches representing proteins annotated as NodD (colored according to cluster table color scheme) and those annotated only as LysR or putatively LysR (black nodes). This initial division shows that bra and bbt nodD1 are possibly not true NodD1 proteins but more general LysR, probably regulating the transcription of other gene systems, e.g., secretion, as both strains have no nodABC genes.
Further exploration of the NodD tree shows that the azc is the most distant in terms of amino acid domain composition with its closest neighbor being bja NodD2. The rest of the proteins in the cluster annotated as Nod largely cluster according to previously determined taxonomic genus relationship, except for rhi NodD1, which more closely aligns with bja NodD1, rather than with its fellow Sinorhizobium species. The largest cluster consists of the NodD1 and NodD2 of sme and smd with the NodD1 of rle, rlg and rlg and NodD2 of rlt. (Figure 3).
In summary, there is a significant difference within this protein cluster between nodulation specific LysR type proteins (NodD proteins) and the other LysR transcription regulation orthologs, indicative of their biochemical roles. Also, NodD orthologs show a slightly different taxonomic relationship compared to 16S rRNA and whole genome approaches.
2.4.2. Other Nodulation Genes
The complexity of Nod factor synthesis and regulation is represented in the current study by two other important gene families, nol and noe. Among important proteins within this class we may cite NoeI, that catalyses the addition of -O-Me fucose to the Nod Factor backbone; NoeE, 3-O-SO3– fucose; NoeL; 3-or 4-O-acetyl fucose and NoeC, involved in the addition of arabinose to the Nod factor [48]. nol gene family is largely predominant in bja, but also abundant in both strains of R. etli and in S. fredii NGR 234 (Table S5), and thus possibly important for the synthesis of specific Nod factors in these species.
Many differences were found in noe clusters (Table S4). Again, the greatest number of genes in this category was found in bja. Sinorhizobium species have only noeA and noeB, and these genes were thought to be specific for Medicago nodulation [50]; however, a noeA ortholog is found in the Trifoliumnodulator rlg as well as the non-symbiont mes. While the functionality of these specific orthologs is not known, this suggests that noeA may not be specific to Medicago.
Protein NolG is ubiquitous, found in cluster 23 and present in all strains from this study. However, it is only annotated as such in sme, with nolG-like genes annotated in smd and rec. Similar to the observations in relation to NodG, the NolG cluster contains many proteins, 130, all belonging to the very broad COG ortholog “COG0841, AcrB, cation/multidrug efflux pump”. Therefore it is possible that several orthologs represent only non-nodulation cation pumps.
Genes 2012 3
154
2.4.3. Bacterial Secretion Systems
After the initial signaling between the host plant and the rhizobia, the next stage controls the progression of the bacteria into the plant and their maturation into nitrogen fixing bacteroids, and many gene families are related to these steps; among the most crucial genes in these stages are the protein secretion systems. Bacterial secretion systems have been classified into seven main groups, Types I through VII, with the fimbrial chaperone-usher pathway forming an additional group. Four of these systems, Types III, IV, V, and VI, assemble surface structures that contact target cells and deliver DNA and/or protein effectors.
The secretion systems found in Rhizobiales range from Type I to Type VI, in addition to the twin-arginine transfer system (Tat). Noteworthy is that different nitrogen fixing Rhizobiales with differing host relationships contain different subsets of these systems [34,51–54]. Previously, it has been reported that only rhi had a suite of secretion systems spanning from Type I–V, which may strongly affect its extraordinary host range [34].
Using BlastlineMCL protein clustering and the KEGG pathway orthology, the number of Type I, II, II, IV, V and VI secretion genes, as well as of exopolysaccharide gene families exo and pss were investigated (Table S7–S14). Interesting, the non-symbiotic mes contains many of these secretion systems, including the virulence related Type IV genes. This could be construed as additional evidence that this strain, or a recent ancestor, was once a symbiont, but lost the symbiotic ability due to the availability of alternate energy sources.
2.4.3.1. Tat, Type I and II Secretion Systems
Tat, Type I and Type II secretion systems are the most simple bacterial secretion systems, excreting proteins into extracellular space without the need of host contact. The twin arginine transport (Tat) system is responsible for transporting pre-folded proteins to the periplasmic space. The Tat pathway has been implicated in many bacterial cellular functions, including motility, biofilm formation, pathogenesis and symbiosis [55]. Protein clusters containing TatA, TatB and TatC were found in all fourteen species (Table S6). For TatA, the basic taxonomic pattern was found with TatA clusters separated roughly according to genera. In contrast, TatB clusters were split between the Azorhizobium/Bradyrhizobium and the other bacteria in a separate cluster, while all TatC proteins fit in one cluster. Therefore, while every species has a Tat system, each one is at least genus specific.
The Type I system is simple and comprises three proteins responsible for the transport of targeted proteins across both bacterial membranes to the extracellular space. This includes ArpD/E, TolC, and the HlyD and HlyB families. In addition, multiple PrtD and PrtE type I proteins have been isolated in rle. As shown in Table S7, ArpD/E, HlyB and PrtDE system proteins are found in the one cluster spanning all fourteen species. Type I secretion is generally common across the fourteen Rhizobiales genomes, but with a notable absence of TolC in rec, rlg, rle and rlt and the lack of KEGG Type I secretion proteins orthologs in mes.
Type II secretion (gsp) was found in Bradyrhizobium, M. loti and Sinorhizobium NGR 234, and absent in the other genomes (Table S9). The other Type II secretion family, sec, was found in all genomes (Table S8). Interesting was the divergence in SecE (preprotein translocase subunit), with twelve different clusters; only rhi, sme and smd secE were positioned in a cluster, while each one of
Genes 2012 3
155
the other genomes occupied a unique cluster. Another contrast was the absence of SecG (preprotein translocase subunit) in rhi, sme and smd, indicating that Sinorhizobium may not contain a preprotein translocase composed of three units.
2.4.3.2. Tat, Type III and IV Secretion Systems
Probably the most important secretion systems in regards to the symbiotic relationship are the host contact dependant Type III and Type IV secretion systems [48,54,56]. Type III secretion system is responsible for producing nodulation outer proteins (Nops), some of which may be delivered into host plant cells via pili on the bacterial surface, and are also closely involved in flagella systems [57]. These Type III systems are present in the KEGG orthology as Ysc. Many species are annotated with different names such as fli and hrc. Amongst the fourteen genomes, Type III protein orthologs are present in bja, mlo, ret, rec and rhi, and absent in rlg, rlt, rle, smd and sme (Table S10). One might assume from these results that the presence of Type III in Sinorhizobium NGR 234 could be implicated in its ability to nodulate the hosts of bja, mlo, ret and rec.
In the Rhizobiales, Type IV secretion proteins are found in two broad families, F-type (Table S11), which includes the virB and trb families, and the P-type cpa/tab/pli system (Table S12). The virB/trb genes are tightly related to virulence and conjugal transfer, while P-type are thought to be adapted from flagella proteins. The trb system was first described in Agrobacterium Ti plasmid as coding for the key virulence system. In the genomes from this study, azc, brj, bbt, mlo and mes contain these genes. The other Rhizobiales have virB orthologs in differing clusters from most of the trb, thus opposed from the A. tumefaciens model. Nonetheless, F-type IV seems to be ubiquitous across the fourteen genomes, including mes, with many of the species having multiple paralogs of many of the virB genes. A similar situation is observed with the P-type secretion mechanism that is found all but azc genome, a further indicator of its relatively recent evolution in nodulation ability.
2.4.3.3. Type V and Type VI Secretion Systems
Type V (auto-transporters) secretion system possesses the simplest secretion apparatus and represents the largest family of protein translocating outer membrane porins in Gram-negative bacteria [58]. Paradoxically, it is not common in the rhizobial genomes studied. Type V is represented in all fourteen gemomes by three orthologs, autA, autB and autC (Table S13), first isolated in rle [21], with mes being the only other genome under study that contained orthologs for all three Aut proteins. The existence of Type V orthologs is further evidence that mes, despite being non-symbiotic, still has virulence or infection potential.
Type VI is a newly discovered system based on bacteriophage secretion systems. First described in 2006, Type VI system has been found in many bacteria, with possible orthologs in mlo, bja and rle [59,60]. A scan of the BlastlineMCL clusters, based on the previous mlo, bja and rle findings [59,60], found possible orthologs also in azc and rec (Table S14). Noteworthy is the fact that rle is the only nitrogen fixer with full sets of Type V and Type VI secretion systems. As both rle and rhi nodulate members of the Viciae tribe, that might suggest some differences in the secretion and communication between microsymbionts and Viciae, and points out that the role of Type V and Type VI secretion systems represent an intriguing question to be explored.
Genes 2012 3
156
2.4.4. Exopolysaccharide Production
Exopolysaccharide production has shown to be critical in host symbiont relationships, e.g., for the initial bacterial invasion that leads to the formation of indeterminate type of nodules on legumes [61]. The examination of exopolysaccharide synthesis and its role in legume infection has been mainly focused on the S. meliloti—Medicago truncatula model, with sme producing two exopolysaccharides, EPS I (succinoglycan) and EPS II (galactoglucan) [46]. In our comparison of genomes two exopolysaccharide synthesis families were surveyed, related to exo and pss genes; these were originally described in S. meliloti and R. leguminosarurm, respectively, and produce alternatively structured EPS I.
In a few cases, the ontology of exopolysaccharide synthesis proteins in nitrogen fixing Rhizobiales seems to be overlapping with four exo and pss terms used interchangeably [21]. For example, exoM is clustered with pssC in the R. etli species, both coding for a glycosyltransferase. This could be either an ontology clash, that the two proteins are in the same cluster due to similar amino acid structure, or that the same single protein is involved in the two systems.
Overall the clustering of exo (Table S15), and pss (Table S16) was similar to the phylogenetic clustering The African nodulator azc has only seven exo and three pss orthologs, compared to the twenty-three and six orthologs, respectively, found in sme. In addition, Bradyrhizobium has also few exo and pps genes, while Mesorhizobium has few pps genes. This interesting comparison could be indicative of a limited EPS I production in these microsymbionts, or that they use different strategies or sets of genes. It cannot be related to the tropical origin or the formation of determinate nodules, as other rhizobia, e.g., the tropical R. etli has several EPS genes and forms determinate nodules in common beans. Still considering the pps family, both ret and rle have twenty pss orthologs. Furthermore, EPS may also play other important roles, such as providing environmental protection, as pointed out in proteomic and transcriptomic studies with B. japonicum [62,63]. Continuing, the Trifolium nodulators have eighteen pss orthologs, missing pssH and pssI. Finally, rec has sixteen pps, missing ppsF, pssH, pssI, pssJ and pssK. In the other genomes the number of pps orthologs range from only three in azc to six in Sinorhizobium.
The role and importance of EPS in the symbiosis has been long discussed and studied. However, the comparison of the genomes has shown that the complexity of the genes regulating EPS is far from being understood. Different species have adopted different sets of genes that seem more related to evolution of the core genome than of the symbiotic genes. Therefore, it can be concluded that the production of exopolysaccharide is not necessarily a feature of a ‘universal’ symbiome.
2.4.5. Nif and Fix Genes
The fixation of nitrogen via nitrogenase requires an anaerobic or micro-aerobic bacteroid environment and the fix gene family is involved in the regulation and metabolism of oxygen in this circumstance. The fix gene family is commonly found in three core operon structures: fixABCX, fixGHIS and fixNOPQ. The first operon is involved in the regulation of gene transcription under low oxygen concentrations. Metabolism of oxygen by the bacteroid occurs via the cytochrome cbb3oxidase complex, a membrane complex encoded by the fixNOPQ operon, that mediates electron exchange and synthesis of ATP via oxidation on the outer surface of the bacteroid membrane. Studies
Genes 2012 3
157
in bja have shown that the second operon, fixGHIS, is required for the initial construction of the cbb3 complex, and like fixNOPQ, is only expressed under micro-aerobic or anaerobic conditions.
BlastlineMCL clustering of the Fix proteins shows both important species distinctions as well as a possible limitation to the algorithm (Table S17). All thirteen symbiotic species have the complete set of genes of the three operons; in the non-symbiont mes, fixABCX is entirely missing, as well as fixQ.
Each different species, except for azc, has a unique fixS ortholog cluster, and mlo has two. However, as the FixS protein is only fifty five amino acids in size, this could also be related to a limitation of the algorithm used by BlastineMCL, adjusted to larger proteins. Another stem nodulator, bbt, has no fixQ ortholog, signifying different cbb3 apparatuses from the structural models already resolved. This diversity of both FixQ and FixS proteins may suggest a diverse range of cbb3 complexes for each species that could result from differences in host nodulation strategies.
The nif family codes for the MoFe-dependant nitrogenase complex, the enzyme required for the catalysis for the nitrogen fixing process [64]. The thirteen symbionts contained, with a higher or lower similarity, the nifBHDKENX operon, which in turn was absent in the non-fixer mes (Table S18). Therefore, along with nod and fix, this species has also lost nif genes.
While a lack of nifX has been previous reported in rle [65], the current analysis has shown that both nifX and nifZ are also absent in R. leguminosarum rlt and rlg. This suggests the MoFe nitrogenase in these leguminosarum species may have a distinct structure from the other Rhizobiales. Also confirmed is the lack of nifQ, required for Mo-incorporation into the complex, in R. leguminosarum, S. meliloti and S. medicae, as well as in the non-symbiotic mes. Consequently, these species should use other means to incorporate Mo into the nitrogenise complex [65,66].
A Nif ortholog cluster was chosen for more in depth analysis of protein alignment (Figure 4). In this example, the NifN/K cluster was examined via neighbor joining (NJ) tree based on BLOSUM62 matrix. Both NifN and NifK (considered structural homologs in regards to their role in nitrogenase complex) split into two clear clades. Unlike much of the NodD cluster, the NifN clade is in agreement with the 16S rRNA phylogeny. Interestingly, the Bradyrhizobium and Azorhizobium NifN orthologs are genetically very distant from the other species, suggesting a different nitrogenase structure. A lower agreement with the 16S rRNA was obtained in the analysis of NifK; more specifically, NifK homologs of rhi show low similarity with other Sinorhizobium NifK homologs, showing higher similarity with mlo and with the R. leguminosarum orthologs. This is another suggestion of an important event of lateral transfer.
2.5. Is it Possible to Define a Symbiome?
As mentioned previously, the definition of a prokaryotic genome is rapidly changing as the number of genomes sequenced and annotated rises. The field of metagenomics has especially caused researchers to re-assess the nature of prokaryotic taxonomy and evolution, for example as a disconnected network topology rather than an exclusively cell and tree centered taxonomy [67]. This is arguably the case for the concept of a “symbiome”. However, the results of this study raise doubts about the definition of a universal “symbiome”: clearly, there are vastly different structures and profound differences in the set of symbiotic regions and genes spanning both chromosomes and plasmids.
Genes 2012 3
158
Figure 4. Phylogeny of NifN/K proteins of the Rhizobiales genomes from this study, achieved through a neighbor joining (NJ) gene tree based on BLOSUM-62 matrix alignment of the proteins in the NifN/K cluster. Number in sequence label is the GENBANK protein GI number. Colored line indicates genus of each genome as coded for in Tables S1 to S18.
The sharply different chromosome and plasmid symmetry taxonomies obtained in the comparison of the fourteen genomes have highlighted a disconnected network pattern caused by lateral transfer within the order Rhizobiales. While chromosome symmetry strongly correlates with genus and species designation, plasmid symmetry is much weaker, especially amongst symbiotic plasmids. This could be construed as evidence of multiple lateral transfer events and rearrangements of core symbiotic genes compared to lesser transfer on other non-symbiotic genes. A good example relies in the symbiotic plasmid of Sinorhizobium NGR 234, that lacks symmetry (e.g., considering the critical protein NodD, Figure 3) with all the other symbiotic plasmid and genome islands analyzed. In addition, rhi has apparently non-Sinorhizobium NifK and NifN proteins (Figure 4). As NGR 234 can nodulate a broad
Genes 2012 3
159
range of legumes, this might suggests a unique re-arrangement of nodulation genes to allow the highest symbiotic ubiquity reported so far.
Protein cluster analysis has shown a much more complex pattern of correlation with host range and protein content, an example being the large array of secretion mechanisms available in the fourteen genomes. Some examples are that the genomes of bja, mlo and rhi contain the majority of Type II secretion proteins, while rle and ret do not contain any. Type III orthologs are found in rec, ret and rhi, but not in R. leguminosarum species, or in the other two Sinorhizobium. All species, except for azc and bra, contain most of the orthologs of Type IV. Intriguingly, rle is the only species with a full complement of both Type V and Type VI secretion orthologs. While NGR 234 (rhi) lacks these Type V and VI secretion proteins, as well as pss exopolysaccharide production enzymes, it can still successfully nodulate both Viciae and Trifollium species [32]. In addition, NGR contains a large number of Type II and III secretion orthologs, indicative of its ability to nodulate the hosts of Bradyrhizobium and Mesorhizobium [32,34]. Interesting, there was an overall lack of secretion genes in azc compared to the other species. One interpretation is that this omission could be related to the capacity of the species to fix nitrogen in free living conditions and only gaining the symbiotic ability in a later stage of its evolution [7]. The non-nitrogen fixing, non symbiont mes demonstrates a reverse situation, evolving from a symbiotic nitrogen fixing ancestor to a chemotroph, with the lack of a symbiotic island i.e., no nif, nodDABC or fixABCX orthologs, but still retaining a wide range of other nod, fix as well as secretion and exopolysaccharide system orthologs typical of symbiotic nitrogen fixing organisms. Altogether, these differences among the fourteen rhizobial genomes highlight the difficulties of defining a “symbiome”.
3. Experimental Section
3.1. Genomes
All fourteen Rhizobiales genomes, including chromosomes and, if applicable, plasmids, were downloaded from NCBI RefSeq. These include three genome sequenced and analyzed by the Center for Rhizobium Studies with the suffix WSM (Western Australian Soil Microbiology Collection). All available nucleotide and protein FASTA files, as well as GENBANK files were utilized. See Table S1 for details.
3.2. Bioinformatics Analysis
Taxonomic analysis of the 16s rRNA gene sequences was completed with MEGA4 [68], by constructing a bootstrapped neighbor joining (NJ) gene tree using Jukes-Cantor substitution. Dotplots (http://code.google.com/p/freckle/) were constructed from the above chromosomal and plasmid nucleotide FASTA files using an in house script. The BLASTMATRIX of all protein sequences and extraction and analysis of KEGG data were performed as outlined in Bellgard et al. 2009 [69].
Construction of phylogenetic NJ trees was based on a CLUSTALW alignment with BLOSUM62 matrix, all accomplished with JALVIEW 2.6.1 [70]. Further editing of trees to publication standard was completed with FigTree v1.3.1 (http://tree.bio.ed.ac.uk/software/figtree/).
Genes 2012 3
160
3.3. Protein Clustering
A protein reciprocal Blast similarity search with a threshold maximum expected value 1e�20 was conducted. This protein clustering used BlastlineMCL (http://www.micans.org/mcl/) program that implements the MCL cluster algorithm for graphs. The granularity of the output cluster was set with an inflation value of 2.5. A bioinformatics workflow was developed that would for each cluster, annotate the cluster based on domain conservation (NCBI CDD), produce a cluster multiple sequence alignment and phylogenic tree for web publication. The clustering analysis can be viewed at the following web site: http://ccg.murdoch.edu.au/organism/rhizobium/RhizobiumSummaries/
The workflow is freely available for researchers interested in high-through put clustering and annotation by contacting [email protected] (reference IVEC and CCG).
4. Concluding Remarks
Overall, it can then be concluded from this study that protein clustering has demonstrated that there are multiple overlapping strategies for nitrogen fixing symbiosis and that perhaps the concept of a single self contained ‘symbiome’ is doubtful. Expanding this protein cluster comparison from Rhizobiales genomes to a larger range of nitrogen fixers could further resolve the symbiome conundrum. To date several species that do not belong to order Rhizobiales but establish nitrogen fixing symbioses have been discovered. These include several species of the beta-proteobacteria Burkholderia [71] and Cupriavidus taiwanensis [72] as well as the non-legume root nodule symbiosis with the Gram positive�Actinomycetales genus Frankia [73]. Therefore, a wider exploration of several classes of bacteria would have to be considered.
This wider approach is demonstrated, in part, by Pini et al. 2011 (92 alphaproteobacterial genomes) [74] and Amadou et al. 2008 (1 betaproteobacterial and 8 alphaproteobacterial genomes) [72]. These studies utilized significantly different clustering techniques and did not include all the 14 strains explored in the current study. However, both these studies share our view, that while there is a large shared gene pool amongst the plant symbionts, there are “multiple recipes” [74] possibly due to the different host environments [72]. This adds further doubt to the concept of a single self-contained “symbiome”.
One must be conscious of the fact that just predicting an ortholog does not guarantee that the said ortholog is actually expressed. Therefore, despite the number of genomes available to be compared, a wider systems biology approach should also be taken into account. This would include symbiont transcriptomics, protein-protein interactions, the effect of the presence of other prokaryotic and eukaryotic species in the rhizosphere, and the genomics and transcriptomics of the plant host itself. Many pertinent studies have already been completed, such as the construction of a S. meliloti interactome [75], the demonstration of host dependant gene expression, based on extensive proteomic and transciptomic analysis in bja [76] and in azc [8], the role of mychorrhizal fungi in the development of nodules [77], and the increasingly complex role of plant nodule-specific cysteine-rich peptides on the symbiotic relationship between legume and bacterium [78], such as host control of R. leguminosarum bacteroid formation through symbiotic auxotrophy [79]. Therefore, if there were any nitrogen fixing ‘symbiome’, it would more likely to be a complex composition of molecular biological and biochemical networks from both symbiont and host in genomics, transcriptomics,
Genes 2012 3
161
proteomics, and even metabolomics. Further, comparative genomics and proteomics, as shown in this study, represents a valuable and key tool for capturing specificities and generalities of each genome, or of groups of genomes showing relevant functionalities, as is the case of nitrogen fixing symbiotic bacteria.
Acknowledgements
We gratefully acknowledge the funding received from Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI and the Centre for Rhizobium Studies (CRS).
M. Hungria is also a fellow from CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico).
References
1. Cheng, Q. Perspectives in biological nitrogen fixation research. J. Integr. Plant Biol. 2008, 50, 786–798.
2. Hungria, M.; Vargas, M.A. Environmental factors affecting N2 fixation in gratn legumes in the tropics, with an emphasis on Brazil. Field Crops Res. 2000, 65, 151–164.
3. Hungria, M.; Loureiro, M.F.; Mendes, I.C.; Campo, R.J.; Graham, P.H. Inoculant Preparation, Production and Application. In Nitrogen Fixation in Agriculture, Forestry, Ecology and the Environment; Werner, W., Newton, W.E., Eds.; Springer: Dordrecht, The Netherlands, 2005; pp. 223–254.
4. Guerrero, G.; Peralta, H.; Aguilar, A.; Diaz, R.; Villalobos, M.A.; Medrano-Soto, A.; Mora, J. Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales. BMC Evol. Biol. 2005, 5, 55–73.
5. Carvalho, F.M.; Souza, R.C.; Barcellos, F.G.; Hungria, M.; Vasconcelos, A.T.R. Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales. BMC Microbiol. 2010, 10, doi:10.1186/1471-2180-10-37.
6. Vavilov, N.I. Centers of origin of cultivated plants. Trends Pract. Bot. Genet. Sel. 1926, 16, 3–248, ( in Russian).
7. Lee, K.B.; de Backer, P.; Aono, T.; Liu, C.T.; Suzuki, S.; Suzuki, T.; Kaneko, T.; Yamada, M.; Tabata, S.; Kupfer, D.M.; et al. The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571. BMC Genomics 2008, 9, doi:10.1186/1471-2164-9-271.
8. Tsukada, S.; Aono, T.; Akiba, N.; Lee, K.B.; Liu, C.T.; Toyazaki, H.; Oyaizu, H. Comparative genome-wide transcriptional profiling of Azorhizobium caulinodans ORS571 grown under free-living and symbiotic conditions. Appl. Environ. Microbiol. 2009, 75, 5037–5046.
9. Kaneko, T.; Nakamura, Y.; Sato, S.; Minamisawa, K.; Uchiumi, T.; Sasamoto, S.; Watanabe, A.; Idesawa, K.; Iriguchi, M.; Kawashima, K.; et al. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 2002, 9, 189–197.
Genes 2012 3
162
10. Bonaldi, K.; Gourion, B.; Fardoux, J.; Hannibal, L.; Cartieaux, F.; Boursot, M.; Vallenet, D.; Chaintreuil, C.; Prin, Y.; Nouwen, N.; et al. Large-scale transposon mutagenesis of photosynthetic Bradyrhizobium sp. strain ORS278 reveals new genetic loci putatively important for nod-independent symbiosis with Aeschynomene indica. Mol. Plant Microbe Interact. 2010, 23, 760–770.
11. Giraud, E.; Moulin, L.; Vallenet, D.; Barbe, V.; Cytryn, E.; Avarre, J.C.; Jaubert, M.; Simon, D.; Cartieaux, F.; Prin, Y.; et al. Legumes symbioses: Absence of nod genes in photosynthetic bradyrhizobia. Science 2007, 316, 1307–1312.
12. Kaneko, T.; Nakamura, Y.; Sato, S.; Asamizu, E.; Kato, T.; Sasamoto, S.; Watanabe, A.; Idesawa, K.; Ishikawa, A.; Kawashima, K.; et al. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res. 2000, 7, 331–338.
13. Bohuslavek, J.; Payne, J.W.; Liu, Y.; Bolton, H.; Xun, L.Y. Cloning, sequencing, and characterization of a gene cluster involved in EDTA degradation from the bacterium BNC1. Appl. Environ. Microbiol. 2001, 67, 688–695.
14. Baldwin, I.L.; Fred, E.B. Nomenclature of the root-nodule bacteria of the Leguminosae. J. Bacteriol. 1929, 17, 141–150.
15. Gonzalez, V.; Bustos, P.; Ramirez-Romero, M.A.; Medrano-Soto, A.; Salgado, H.; Hernandez-Gonzalez, I.; Hernandez-Celis, J.C.; Quintero, V.; Moreno-Hagelsieb, G.; Girard, L.; et al. The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments. Genome Biol. 2003, 4, doi:10.1186/gb-2003-4-6-r36.
16. González, V.; Santamaría, R.I.; Bustos, P.; Hernández-González, I.; Medrano-Soto, A.; Moreno-Hagelsieb, G.; Janga, S.C.; Ramírez, M.A.; Jiménez-Jacinto, V.; Collado-Vides, J.; et al. The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons. Proc. Natl. Acad. Sci. USA 2006, 103, 3834–3839.
17. González, V.; Acosta, J.L.; Santamaría, R.I.; Bustos, P.; Fernández, J.L.; Hernández González, I.L.; Díaz, R.; Flores, M.; Palacios, R.; Mora, J.; et al. Conserved symbiotic plasmid DNA sequences in the multireplicon pangenomic structure of Rhizobium etli. Appl. Environ. Microbiol. 2010, 76, 1604–1614.
18. Lozano, L.; Hernández-González, I.; Bustos, P.; Santamaría, R.I.; Souza, V.; Young, J.P.W.; Dávila, G.; González, V. Evolutionary dynamics of insertion sequences in relation to the evolutionary histories of the chromosome and symbiotic plasmid genes of Rhizobium etli populations. Appl. Environ. Microbiol. 2010, 76, 6504–6513.
19. Howieson, J.G.; Yates, R.J.; Ryder, M.; Real, D. The interactions of Rhizobium leguminosarum biovar trifolii in nodulation of annual and perennial Trifolium spp. from diverse centres of origin. Aust. J. Exp. Agric. 2005, 45, 199–207.
20. Yates, R.; Howieson, J.; Reeve, W.; O’Hara, G. A re-appraisal of the biology and terminology describing rhizobial strain success in nodule occupancy of legumes in agriculture. Plant Soil 2011, 348, 255–267.
21. Young, J.P.; Crossman, L.; Johnston, A.; Thomson, N.; Ghazoui, Z.; Hull, K.; Wexler, M.; Curson, A.; Todd, J.; Poole, P.; et al. The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol. 2006, 7, doi:10.1186/gb-2006-7-4-r34.
Genes 2012 3
163
22. Chen, W.X.; Yan, G.H.; Li, J.L. Numerical taxonomic study of fast-growing soybean rhizobia and a proposal that Rhizobium fredii be assigned to Sinorhizobium gen. nov. Int. J. Syst. Bacteriol. 1988, 38, 392–397.
23. Young, J.M. The genus name Ensifer Casida 1982 takes priority over Sinorhizobium Chen et al. 1988, and Sinorhizobium morelense Wang et al. 2002 is a later synonym of Ensfer adhaerens Casida 1982. Is the combination ‘Sinorhizobium adhaerens’ (Casida 1982) Willems et al. 2003 legitimate? Request for an Opinion. Int. J. Syst. Evol. Microbiol. 2003, 53, 2107–2110.
24. Sawada, H.; Kuykendall, L.D.; Young, J.M. Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. J. Gen. Appl. Microbiol. 2003, 49, 155–179.
25. Graham, P.H. Ecology of the Root-Nodule Bacteria of Legumes. In Nitrogen-Fixing Leguminous Symbioses; Dilworth, M.J., James, E.K., Sprent, J.I., Newton, W.E., Eds.; Springer: Dordrecht, The Netherlands, 2007; volume 7, pp. 23–58.
26. Capela, D.; Barloy-Hubler, F.; Gouzy, J.; Bothe, G.; Ampe, F.; Batut, J.; Boistard, P.; Becker, A.; Boutry, M.; Cadieu, E.; et al. Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021. Proc. Natl. Acad. Sci. USA 2001, 98, 9877–9882.
27. Barnett, M.J.; Fisher, R.F.; Jones, T.; Komp, C.; Abola, A.P.; Gurjal, M.; Hong, A.; Huizar, L.; Bowser, L.; Capela, D.; et al. Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc. Natl. Acad. Sci. USA 2001, 98, 9883–9888.
28. Finan, T.M.; Weidner, S.; Wong, K.; Buhrmester, J.; Chain, P.; Vorholter, F.J.; Hernandez-lucas, I.; Becker, A.; Cowie, A.; Gouzy, J.; et al. The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti. Proc. Natl. Acad. Sci. USA 2001, 98, 9889–9894.
29. Terpolilli, J.J.; Tiwari, R.P.; Dilworth, M.J.; O'Hara, G.W.; Howieson, J.G. Investigating nitrogen fixation in the Medicago-Sinorhizobium symbiosis. Biol. Nitrogen Fixat. 2008, 42, 145–146.
30. Terpolilli, J.J.; O'Hara, G.W.; Tiwari, R.P.; Dilworth, M.J.; Howieson, J.G. The model legume Medicago truncatula A17 is poorly matched for N2 fixation with the sequenced microsymbiont Sinorhizobium meliloti 1021. New Phytol. 2008, 179, 62–66.
31. Garau, G.; Reeve, W.G.; Brau, L.; Deiana, P.; Yates, R.J.; James, D.; Tiwari, R.; O’Hara, G.W.; Howieson, J.G. The symbiotic requirements of different Medicago spp. suggest the evolution of Sinorhizobium meliloti and S-Medicae with hosts differentially adapted to soil pH. Plant Soil 2005, 276, 263–277.
32. Pueppke, S.G.; Broughton, W.J. Rhizobium sp. strain NGR234 and R. fredii USDA257 share exceptionally broad, nested host ranges. Mol. Plant Microbe Interact. 1999, 12, 293–318.
33. Viprey, V.; Rosenthal, A.; Broughton, W.J.; Perret, X. Genetic snapshots of the Rhizobium species NGR234 genome. Genome Biol. 2000, 1, 1–17.
34. Schmeisser, C.; Liesegang, H.; Krysciak, D.; Bakkou, N.; le Quéré, A.; Wollherr, A.; Heinemeyer, I.; Morgenstern, B.; Pommerening-Röser, A.; Flores, M.; et al. Rhizobium sp. strain NGR234 possesses a remarkable number of secretion systems. Appl. Environ. Microbiol. 2009, 75, 4035–4045.
35. Turner, S.L.; Zhang, X.X.; Li, F.D.; Young, J.P. What does a bacterial genome sequence represent? Mis-assignment of MAFF 303099 to the genospecies Mesorhizobium loti. Microbiology 2002, 148, 3330–3331.
Genes 2012 3
164
36. Willems, A. The taxonomy of rhizobia: An overview. Plant and Soil 2006, 287, 3–14. 37. Landeta, C.; Davalos, A.; Cevallos, M.A.; Geiger, O.; Brom, S.; Romero, D. Plasmids with a
chromosome-like role in Rhizobium. J. Bacteriol. 2011, 193, 1317–1326. 38. Harrison, P.W.; Lower, R.P.J.; Kim, N.K.D.; Young, J.P.W. Introducing the bacterial ‘chromid’:
Not a chromosome, not a plasmid. Trends Microbiol. 2010, 18, 141–148. 39. Gevers, D.; Cohan, F.M.; Lawrence, J.G.; Spratt, B.G.; Coenye, T.; Feil, E.J.; Stackebrandt, E.;
Peer, Y.V.D.; Vandamme, P.; THOMPSON, F.L.; et al. Re-evaluating prokaryotic species. Nat. Rev. Microbiol. 2005, 3, 733–739.
40. Gogarten, J.P.; Townsend, J.P. Horizontal gene transfer, genomes innovation and evolution. Nat. Rev. Microbiol. 2005, 3, 679–687.
41. Gómez-Hernández, N.; Reyes-González, A.; Sánchez, C.; Mora, Y.; Delgado, M.J.; Girard, L. Regulation and symbiotic role of nirK and norC expression in Rhizobium etli. Mol. Plant Microbe Interact. 2011, 24, 233–235.
42. Enright, A.J.; van Dongen, S.; Ouzounis, C.A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002, 30, 1575–1584.
43. Nicolás, M.F.; Barcellos, M.F.; Hess, P.N.; Hungria, M. ABC transporters in Mycoplasma hyopneumoniae and Mycoplasma synoviae: Insights into evolution and pathogenicity. Genet.Mol. Biol. 2007, 30, 202–211.
44. Kaneko, T.; Nakamura, Y.; Sato, S.; Asamizu, E.; Kato, T.; Sasamoto, S.; Watanabe, A.; Idesawa, K.; Ishikawa, A.; Kawashima, K.; et al. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti (supplement). DNA Res. 2000, 7, 381–406.
45. Galibert, F.; Finan, T.M.; Long, S.R.; Puhler, A.; Abola, P.; Ampe, F.; Barloy-Hubler, F.; Barnett, M.J.; Becker, A.; Boistard, P.; et al. The composite genome of the legume symbiont Sinorhizobium meliloti. Science 2001, 293, 668–672.
46. Jones, K.M.; Kobayashi, H.; Davies, B.W.; Taga, M.E.; Walker, G.C. How rhizobial symbionts invade plants: The Sinorhizobium–Medicago model. Nat. Rev. Microbiol. 2007, 5, 619–633.
47. Oliveira, L.R.; Marcelino, F.C.; Barcellos, F.G.; Rodrigues, E.P.; Megías, M.; Hungria, M. The nodC, nodG, and glgX genes of Rhizobium tropici strain PRF 81. Funct. Integr. Genomics 2010, 10, 425–431.
48. Downie, J.A. The roles of extracellular proteins, polysaccharides and signals in the interactions of rhizobia with legume roots. FEMS Microbiol. Rev. 2010, 34, 150–170.
49. Walker, S.A.; Viprey, V.; Downie, J.A. Dissection of nodulation signaling using pea mutants defective for calcium spiking induced by nod factors and chitin oligomers. Proc. Natl. Acad. Sci. USA 2000, 97, 13413–13418.
50. Vlassak, K.M.; de Wilde, P.; Snoeck, C.; Luyten, E.; van Rhijn, P.; Vanderleyden, J. The Rhizobium sp. BR816 nodD3 gene is regulated by a transcriptional regulator of the AraC/XylS family. Mol. Gen. Genet. 1998, 258, 558–561.
51. Cooper, J.E. Multiple responses of rhizobia to flavonoids during legume root infection. Adv. Bot. Res. Inc. Adv. Plant Pathol. 2004, 41, 1–62.
52. Cooper, J.E. Early interactions between legumes and rhizobia: Disclosing complexity in a molecular dialogue. J. Appl. Microbiol. 2007, 103, 1355–1365.
Genes 2012 3
165
53. Fauvart, M.; Michiels, J. Rhizobial secreted proteins as determinants of host specificity in the rhizobium-legume symbiosis. FEMS Microbiol. Lett. 2008, 285, 1–9.
54. Deakin, W.J.; Broughton, W.J. Symbiotic use of pathogenic strategies: Rhizobial protein secretion systems. Nat. Rev. Microbiol. 2009, 7, 312–320.
55. Pickering, B.S.; Oresnik, I.J. The twin arginine transport system appears to be essential for viability in Sinorhizobium meliloti. J. Bacteriol. 2010, 192, 5173–5180.
56. Alvarez-Martinez, C.E.; Christie, P.J. Biological diversity of prokaryotic type IV secretion systems. Microbiol. Mol. Biol. Rev. 2009, 73, 775–808.
57. Krishnan, H.B.; Lorio, J.; Kim, W.S.; Jiang, G.Q.; Kim, K.Y.; DeBoer, M.; Pueppke, S.G. Extracellular proteins involved in soybean cultivar-specific nodulation are associated with pilus-like surface appendages and exported by a type III protein secretion system in Sinorhizobium fredii USDA257. Mol. Plant Microbe Interact. 2003, 16, 617–625.
58. Desvaux, M.; Parham, N.J.; Henderson, I.R. Type V protein secretion: Simplicity gone awry? Curr. Issues Mol. Biol. 2004, 6, 111–124.
59. Schwarz, S.; Hood, R.D.; Mougous, J.D. What is type VI secretion doing in all those bugs? Trends Microbiol. 2010, 18, 531–537.
60. Bonemann, G.; Pietrosiuk, A.; Mogk, A. Tubules and donuts: A type VI secretion story. Mol. Microbiol. 2010, 76, 815–821.
61. Skorupska, A.; Janczarek, M.; Marczak, M.; Mazur, A.; Król, J. Rhizobial exopolysaccharides: Genetic control and symbiotic functions. Microbial Cell Factories 2006, 5, doi:10.1186/1475-2859-5-7.
62. Cytryn, E.J.; Sangurdekar, D.P.; Streeter, J.G.; Franck, W.L.; Chang, W.-S.; Stacey, G.; Emerich, D.W.; Joshi, T.; Xu, D.; Sadowsky, M.J. Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress. J. Bacteriol. 2007, 189, 6751–6762.
63. Batista, J.S.S.; Torres, A.R.; Hungria, M. Towards a two-dimensional proteomic reference map of Bradyrhizobium japonicum CPAC 15: Spotlighting on “hypothetical proteins”. Proteomics 2010, 10, 3176–3189.
64. Raymond, J.; Siefert, J.L.; Staples, C.R.; Blankenship, R.E. The natural history of nitrogen fixation. Mol. Biol. Evol. 2004, 21, 541–554.
65. Masson-Boivin, C.; Giraud, E.; Perret, X.; Batut, J. Establishing nitrogen-fixing symbiosis with legumes: How many rhizobium recipes? Trends Microbiol. 2009, 17, 458–466.
66. Rubio, L.M.; Ludden, P.W. Biosynthesis of the iron-molybdenum cofactor of nitrogenase. Annu. Rev. Microbiol. 2008, 62, 93–111.
67. Halary, S.; Leigh, J.W.; Cheaib, B.; Lopez, P.; Bapteste, E. Network analyses structure genetic diversity in independent genetic worlds. Proc. Natl. Acad. Sci. USA 2010, 107, 127–132.
68. Kumar, S.; Nei, M.; Dudley, J.; Tamura, K. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 2008, 9, 299–306.
69. Bellgard, M.I.; Wanchanthuek, P.; La, T.; Ryan, K.; Moolhuijzen, P.; Albertyn, Z.; Shaban, B.; Motro, Y.; Dunn, D.S.; Schibeci, D.; et al. Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine. Plos One 2009, 4, doi:10.1371/journal.pone.0004641.
Genes 2012 3
166
70. Waterhouse, A.M.; Procter, J.B.; Martin, D.M.; Clamp, M.; Barton, G.J. Jalview Version 2—A multiple sequence alignment editor and analysis workbench. Bioinformatics 2009, 25, 1189–1191.
71. Garau, G.; Yates, R.; Deiana, P.; Howieson, J. Novel strains of nodulating Burkholderia have a role in nitrogen fixation with papilionoid herbaceous legumes adapted to acid, infertile soils. Soil Biol. Biochem. 2009, 41, 125–134.
72. Amadou, C.; Pascal, G.; Mangenot, S.; Glew, M.; Bontemps, C.; Capela, D.; Carrère, S.; Cruveiller, S.; Dossat, C.; Lajus, A.; et al. Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res. 2008, 18, 1472–1483.
73. Pokharel, A.; Mirza, B.S.; Dawson, J.O.; Hahn, D. Frankia populations in soil and root nodules of sympatrically grown Alnus taxa. Microb. Ecol. 2011, 61, 92–100.
74. Pini, F.; Galardini, M.; Bazzicalupo, M.; Mengoni, A. Plant-bacteria association and symbiosis: Are there common genomic traits in alphaproteobacteria? Genes 2011, 2, 1017–1032.
75. Rodriguez-llorente, I.; Caviedes, M.A.; Dary, M.; Palomares, A.J. The symbiosis interactome: A computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti. BMC Syst. Biol. 2009, 3, 1–18.
76. Delmotte, N.; Ahrens, C.; Knief, C.; Qeli, E.; Koch, M. An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules. Proteomics 2010, 10, 1391–1400.
77 Ballesteros-Almanza, L.; Altamirano-Hernandez, J.; Pena-Cabriales, J.J.; Santoyo, G.; Sanchez-Yanez, J.M.; Valencia-Cantero, E.; Macias-Rodriguez, L.; Lopez-Bucio, J.; Cardenas-Navarro, R.; Farias-Rodriguez, R. Effect of co-inoculation with mycorrhiza and rhizobia on the nodule trehalose content of different bean genotypes. Open Microbiol. J. 2010, 4, 83–92.
78 Batut, J.; Mergaert, P.; Masson-Boivin, C. Peptide signalling in the rhizobium-legume symbiosis. Current Opinion in Microbiology 2011, 14, 181–187.
79 Prell, J.; Bourdès, A.; Kumar, S.; Lodwig, E.; Hosie, A.; Kinghorn, S.; White, J.; Poole, P. Role of symbiotic auxotrophy in the Rhizobium-legume symbioses. Plos One 2010, 5, doi:10.1371/journal.pone.0013933.
© 2012 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).�
Supplementary Files
Figure S1. FRECKLE DNA dotplot of the fourteen Rhizobiales plasmids, constructed from nucleotide FASTA files using an in house script.
Tables S1 to S18—Assorted gene clusters from blastlinemcl analysis.
Table S1. Full table of KEGG pathways of the fourteen genomes.
Relevant KEGG Pathways KEGG ORTHOLOGS
azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
1. Metabolism 1048 1253 1357 1338 1225 1036 1079 1253 1052 1072 1315 1079 1079 1230
1.1 Carbohydrate Metabolism 240 295 295 296 274 245 249 279 257 256 299 262 267 273
ko00010 Glycolysis/Gluconeogenesis 21 26 27 25 25 22 20 22 20 20 24 22 24 26 ko00020 Citrate cycle (TCA cycle) 21 24 23 23 23 22 22 21 22 23 22 22 21 21 ko00620 Pyruvate metabolism 33 33 34 32 30 31 29 30 27 28 33 26 30 28 ko00030 Pentose phosphate pathway 19 25 25 24 25 25 22 22 23 23 24 26 25 25 ko00040 Pentose and glucuronate interconversions 13 13 12 10 13 11 13 18 15 13 20 13 15 17 ko00051 Fructose and mannose metabolism 8 17 18 18 20 10 8 15 9 8 16 12 10 15 ko00520 Amino sugar and nucleotide sugar metabolism 19 25 24 27 24 22 22 27 24 24 28 25 23 28 ko00052 Galactose metabolism 6 10 8 10 12 10 12 14 14 13 14 11 10 13 ko00500 Starch and sucrose metabolism 12 18 19 19 14 13 19 23 20 21 22 19 16 5 ko00053 Ascorbate and aldarate metabolism 6 7 7 7 4 5 5 7 6 5 6 6 7 6 ko00630 Glyoxylate and dicarboxylate metabolism 26 30 26 29 22 21 21 22 22 22 26 23 25 26 ko00640 Propanoate metabolism 23 26 30 27 22 20 20 21 20 21 26 20 24 22 ko00562 Inositol phosphate metabolism 4 4 7 8 8 6 9 9 8 8 9 8 9 9 ko00650 Butanoate metabolism 22 31 28 30 25 21 21 22 21 21 23 23 22 26 ko00660 C5-Branched dibasic acid metabolism 7 6 7 7 7 6 6 6 6 6 6 6 6 6 1.2 Energy Metabolism 114 147 146 145 113 114 112 111 99 99 118 111 124 138
ko00910 Nitrogen metabolism 26 33 30 28 21 17 18 27 18 20 22 27 27 30 ko00195 Photosynthesis - - 8 8 - - - - - - - - - - ko00190 Oxidative phosphorylation 52 50 51 52 50 50 47 48 47 47 51 47 47 49 ko00680 Methane metabolism 27 17 18 18 16 10 10 12 10 10 16 12 11 16 ko00920 Sulfur metabolism 9 11 10 11 9 9 8 9 8 8 10 9 9 12
Table S1. Cont.
Relevant KEGG Pathways KEGG ORTHOLOGS
azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
1.2 Energy Metabolism 114 147 146 145 113 114 112 111 99 99 118 111 124 138
ko00720 Reductive carboxylate cycle (CO2 fixation) - 17 17 17 - 13 14 - - - - - 12 12 ko00710 Carbon fixation in photosynthetic organisms - 19 20 19 17 15 15 15 16 14 19 16 18 19 1.3 Lipid Metabolism 52 63 72 72 72 53 61 76 58 57 81 56 58 71
ko00061 Fatty acid biosynthesis 12 13 13 13 13 13 14 13 13 13 13 14 13 13 ko00071 Fatty acid metabolism 11 14 13 13 13 11 9 13 8 8 12 8 9 12 ko00072 Synthesis and degradation of ketone bodies 4 6 4 5 3 2 2 2 2 2 3 3 3 3 ko00100 Steroid biosynthesis - - 1 1 - - - - - - - 1 - - ko00120 Primary bile acid biosynthesis - 1 1 1 2 - - - - - 2 - - - ko00121 Secondary bile acid biosynthesis 1 - - - 1 - - - - - 1 - - - ko00140 Steroid hormone biosynthesis - 1 2 - 3 - - 1 - - 3 - - 2 ko00564 Glycerophospholipid metabolism 14 17 19 18 17 15 18 20 17 17 23 14 15 16 ko00565 Ether lipid metabolism - - 1 1 - - - 1 - - 3 - - - ko00590 Arachidonic acid metabolism - 2 3 3 1 1 2 3 2 2 2 1 1 1 ko00600 Sphingolipid metabolism - 1 1 1 3 - 1 2 2 1 4 2 1 4 ko01040 Biosynthesis of unsaturated fatty acids 3 6 6 5 5 4 5 7 6 6 6 4 5 6 ko00591 Linoleic acid metabolism - 1 1 1 1 - - 1 - - 1 - - 1 ko00592 alpha-Linolenic acid metabolism 1 - - - 1 1 - 1 - - 1 - - 1 ko00561 Glycerolipid metabolism 6 8 7 10 12 6 10 13 10 10 13 9 11 12 1.4 Nucleotide Metabolism 102 96 100 99 111 105 100 108 97 99 112 97 98 114
ko00240 Pyrimidine metabolism 42 39 40 37 44 40 41 44 39 42 44 38 39 44 ko00230 Purine metabolism 60 57 60 62 67 65 59 64 58 57 68 59 59 70 1.5 Amino Acid Metabolism 221 249 268 258 275 224 235 261 227 241 272 239 236 253
ko00250 Alanine, aspartate and glutamate metabolism 21 23 21 20 21 19 22 23 22 23 24 23 22 22 ko00260 Glycine, serine and threonine metabolism 29 26 32 30 40 29 32 35 30 33 35 33 31 35
Table S1. Cont.
Relevant KEGG Pathways KEGG ORTHOLOGS
azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
1.5 Amino Acid Metabolism 221 249 268 258 275 224 235 261 227 241 272 239 236 253
ko00290 Valine, leucine and isoleucine biosynthesis 16 16 16 16 16 16 15 15 15 15 15 15 15 15 ko00270 Cysteine and methionine metabolism 16 21 25 21 25 18 19 21 19 18 23 19 22 22 ko00280 Valine, leucine and isoleucine degradation 19 23 19 21 20 18 12 19 15 17 20 19 21 21 ko00300 Lysine biosynthesis 16 13 14 14 12 12 12 12 11 12 13 12 12 12 ko00310 Lysine degradation 9 10 10 10 11 8 10 11 9 10 11 9 9 9 ko00330 Arginine and proline metabolism 30 34 38 35 39 34 40 36 34 36 41 37 38 38 ko00340 Histidine metabolism 13 17 19 18 20 16 16 19 16 16 19 17 15 17
ko00350 Tyrosine metabolism 12 19 23 22 17 17 12 21 11 14 18 14 10 15 ko00360 Phenylalanine metabolism 11 14 16 15 17 8 14 15 14 14 17 13 11 14 ko00380 Tryptophan metabolism 12 16 16 16 16 10 12 13 12 13 13 11 12 13 ko00400 Phenylalanine, tyrosine and tryptophan biosynthesis 17 17 19 20 21 19 19 21 19 20 23 17 18 20 1.6 Metabolism of Other Amino Acids 50 58 62 57 60 48 54 58 54 57 58 56 54 62
ko00410 beta-Alanine metabolism 7 10 13 11 12 8 9 10 9 9 11 11 9 10 ko00430 Taurine and hypotaurine metabolism 3 5 4 3 4 4 4 4 4 5 3 3 5 7 ko00440 Phosphonate and phosphinate metabolism 2 4 4 4 4 2 3 3 3 3 3 2 3 4 ko00450 Selenoamino acid metabolism 12 12 12 11 15 11 11 14 11 11 12 12 11 15 ko00460 Cyanoamino acid metabolism 6 7 6 5 4 4 6 6 6 7 6 5 5 5 ko00471 D-Glutamine and D-glutamate metabolism 4 4 5 5 4 3 4 4 4 4 5 5 4 4 ko00472 D-Arginine and D-ornithine metabolism 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ko00473 D-Alanine metabolism 3 3 3 3 3 3 3 3 3 3 3 3 3 3 ko00480 Glutathione metabolism 12 12 14 14 13 12 13 13 13 14 14 14 13 13 1.7 Glycan Biosynthesis and Metabolism 30 29 31 33 32 25 33 35 32 34 36 31 22 32
ko00510 N-Glycan biosynthesis - 1 1 1 1 - 1 1 - 1 1 - - - ko00531 Glycosaminoglycan degradation - - - - - - 1 1 1 1 2 1 1 1
Table S1. Cont.
Relevant KEGG Pathways KEGG ORTHOLOGS
azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
1.7 Glycan Biosynthesis and Metabolism 30 29 31 33 32 25 33 35 32 34 36 31 22 32
ko00603 Glycosphingolipid biosynthesis—globo series - - - 1 1 - 2 2 2 2 2 2 2 2 ko00604 Glycosphingolipid biosynthesis—ganglio series - - - - - - 1 1 1 1 1 1 1 1 ko00540 Lipopolysaccharide biosynthesis 15 12 14 15 14 9 9 9 9 10 9 9 - 9 ko00550 Peptidoglycan biosynthesis 15 16 16 16 16 16 16 16 16 16 16 16 16 16
ko00511 Other glycan degradation - - - - - - 3 5 3 3 5 2 2 3 1.8 Metabolism of Cofactors and Vitamins 117 132 143 137 131 103 122 126 114 117 130 119 117 124
ko00730 Thiamine metabolism 10 11 11 11 10 9 11 11 8 11 12 9 9 10 ko00740 Riboflavin metabolism 9 7 9 9 9 7 7 10 7 7 9 6 7 8 ko00750 Vitamin B6 metabolism 6 6 5 5 6 6 6 5 6 6 7 6 6 6 ko00760 Nicotinate and nicotinamide metabolism 13 16 14 13 17 16 15 17 14 15 17 15 16 16 ko00770 Pantothenate and CoA biosynthesis 14 16 16 13 17 14 13 15 14 13 15 14 13 15 ko00780 Biotin metabolism 2 6 6 2 5 1 1 1 1 1 1 5 1 1 ko00785 Lipoic acid metabolism 2 2 2 2 2 2 2 2 2 2 2 2 2 2 ko00790 Folate biosynthesis 9 9 7 7 9 8 10 10 8 8 9 9 9 9 ko00670 One carbon pool by folate 13 11 12 12 11 13 13 13 12 13 13 11 11 12 ko00830 Retinol metabolism - 2 2 2 2 2 2 2 1 1 2 2 2 2 ko00130 Ubiquinone and other terpenoid-quinone biosynthesis 7 10 8 8 6 9 7 6 7 7 8 8 8 8 ko00860 Porphyrin and chlorophyll metabolism 32 36 51 53 37 16 35 34 34 33 35 32 33 35 1.9 Biosynthesis of Polyketides and Terpenoids 29 29 42 43 29 27 28 36 28 27 34 27 27 34
ko01051 Biosynthesis of ansamycins - 1 2 1 1 1 1 2 1 1 2 1 1 2 ko00253 Tetracycline biosynthesis - 4 4 4 4 4 4 4 4 4 4 4 4 4 ko00523 Polyketide sugar unit biosynthesis 4 1 4 4 4 4 4 4 4 4 4 4 4 4 ko01053 Biosynthesis of siderophore group nonribosomal peptides
- 1 1 1 - - 1 1 1 1 1 2 1 1
Table S1. Cont.
Relevant KEGG Pathways KEGG ORTHOLOGS
azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
1.9 Biosynthesis of Polyketides and Terpenoids 29 29 42 43 29 27 28 36 28 27 34 27 27 34
ko01055 Biosynthesis of vancomycin group antibiotics - 1 1 1 1 1 1 1 1 1 1 1 1 1 ko00900 Terpenoid backbone biosynthesis 10 10 12 12 10 10 11 12 10 10 10 10 10 10 ko00903 Limonene and pinene degradation 15 9 12 12 7 5 4 10 5 4 10 3 4 10 ko00908 Zeatin biosynthesis - 1 1 1 1 1 1 1 1 1 1 1 1 1 ko00906 Carotenoid biosynthesis - 1 5 7 1 1 1 1 1 1 1 1 1 1 1.10 Biosynthesis of Other Secondary Metabolites 8 21 32 35 31 20 27 34 26 26 37 26 23 28
ko00940 Phenylpropanoid biosynthesis - 2 2 2 1 1 3 3 3 3 3 3 2 2 ko00945 Stilbenoid, diarylheptanoid and gingerol biosynthesis - 1 1 1 1 - - 1 - - 1 - - 1 ko00941 Flavonoid biosynthesis - 1 2 2 - - - 1 1 1 2 - - - ko00901 Indole alkaloid biosynthesis - - - - - - - 1 - - - - - - ko00950 Isoquinoline alkaloid biosynthesis - 2 4 4 5 1 3 4 3 3 5 3 2 3 ko00960 Tropane, piperidine and pyridine alkaloid biosynthesis
- 5 7 8 5 3 4 6 4 4 8 4 4 4
ko00232 Caffeine metabolism - - 1 1 1 - 1 1 - - - - - 1 ko00965 Betalain biosynthesis - - - - 1 - - 1 - - - 1 - - ko00311 Penicillin and cephalosporin biosynthesis - 1 1 2 2 1 2 1 2 2 2 1 1 1 ko00312 beta-Lactam resistance - 1 1 1 1 1 1 1 1 1 1 1 1 ko00521 Streptomycin biosynthesis 6 4 8 9 8 8 9 9 8 8 8 8 9 9 ko00901 Indole alkaloid biosynthesis - - - - 1 - - - - - - 1 - - ko00524 Butirosin and neomycin biosynthesis - 1 1 1 1 1 1 1 1 1 1 1 1 1 ko00401 Novobiocin biosynthesis 2 3 4 4 5 4 3 4 3 3 6 3 3 5 1.11 Xenobiotics Biodegradation and Metabolism 85 134 166 163 97 72 58 129 60 59 138 55 53 101
ko00930 Caprolactam degradation 2 5 5 4 3 3 4 5 4 4 5 3 3 4
Table S1. Cont.
Relevant KEGG Pathways KEGG ORTHOLOGS
azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
1.11 Xenobiotics Biodegradation and Metabolism 85 134 166 163 97 72 58 129 60 59 138 55 53 101
ko00621 Biphenyl degradation 2 - 1 1 - - 1 2 1 1 2 - - - ko00622 Toluene and xylene degradation - 6 10 8 3 2 1 5 2 2 7 1 - 3 ko00361 gamma-Hexachlorocyclohexane degradation 4 10 10 11 7 2 3 11 3 3 12 3 2 6 ko00641 3-Chloroacrylic acid degradation - 5 5 5 5 4 3 5 2 2 5 3 3 4 ko00351 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
- 1 3 3 - 1 - 2 - - - - - 1
ko00623 2,4-Dichlorobenzoate degradation 7 9 9 8 3 4 3 5 3 3 4 3 3 3 ko00631 1,2-Dichloroethane degradation - 5 4 4 3 2 2 4 2 2 3 2 2 3 ko00625 Tetrachloroethene degradation 7 4 4 4 4 3 4 3 3 4 3 3 4 ko00643 Styrene degradation 4 9 8 8 6 5 4 5 4 4 7 5 4 5 ko00627 1,4-Dichlorobenzene degradation 14 6 7 8 4 2 2 5 3 3 8 3 2 4 ko00626 Naphthalene and anthracene degradation 4 6 9 9 5 3 - 8 - - 8 - - 6 ko00642 Ethylbenzene degradation 2 1 1 1 2 1 - 2 - - 2 - - 2 ko00628 Fluorene degradation - 4 7 6 3 2 1 4 1 1 5 1 1 3 ko00629 Carbazole degradation - 1 2 3 - - - 1 1 1 2 1 - - ko00632 Benzoate degradation via CoA ligation - 17 18 18 12 10 11 14 11 11 14 10 11 14 ko00362 Benzoate degradation via hydroxylation 20 17 23 23 12 12 10 17 10 9 20 6 8 12 ko00791 Atrazine degradation 3 5 7 6 3 3 3 6 4 4 6 3 3 4 ko00363 Bisphenol A degradation - 2 4 4 2 - - 3 - - 3 - - 3 ko00624 1- and 2-Methylnaphthalene degradation 4 9 11 12 8 6 2 10 1 1 9 2 2 10 ko00633 Trinitrotoluene degradation 6 5 7 7 5 3 2 2 1 1 3 2 3 2 ko00281 Geraniol degradation 3 4 6 6 5 5 2 6 2 2 5 2 2 6 ko00364 Fluorobenzoate degradation 3 3 5 4 2 2 1 3 2 2 4 2 1 2
Table S1. Cont.
Relevant KEGG Pathways KEGG ORTHOLOGS
azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
2. Genetic Information Processing 247 249 241 242 240 231 239 240 244 242 241 234 242 245
2.1 Transcription 4 4 4 4 4 4 4 4 4 4 4 4 4 4
ko03020 RNA polymerase 4 4 4 4 4 4 4 4 4 4 4 3 4 4 2.2 Translation 134 131 128 129 130 123 128 128 129 129 127 124 129 132
ko03010 Ribosome 57 54 53 54 57 54 54 54 54 54 51 52 54 57 ko00970 Aminoacyl-tRNA biosynthesis 47 46 47 47 46 44 46 46 47 47 47 45 47 47 ko03060 Protein export 16 17 16 16 14 15 15 15 15 15 15 14 15 15 ko03018 RNA degradation 14 14 12 12 13 10 13 13 13 13 14 13 13 13 2.3 Folding, Sorting and Degradation 40 40 38 38 36 34 36 37 38 38 37 36 38 38
ko03060 Protein Export 16 17 17 17 14 15 15 15 16 16 15 14 16 16 ko04122 Sulfur relay system 10 9 9 9 9 9 8 8 8 8 8 8 8 8 ko03018 RNA degredation 14 14 12 12 13 10 13 14 14 14 14 14 14 14 2.4 Replication and Repair 69 74 71 71 70 70 71 71 73 71 73 70 71 71
ko03030 DNA replication 14 14 14 14 14 14 14 14 14 14 14 14 14 14 ko03410 Base excision repair 10 13 12 12 11 11 12 12 13 12 13 11 12 12 ko03420 Nucleotide excision repair 8 8 8 8 8 8 8 8 8 8 8 8 8 8 ko03430 Mismatch repair 16 17 16 16 16 16 16 16 17 16 17 16 16 16 ko03440 Homologous recombination 19 20 19 19 19 19 19 19 19 19 19 19 19 19 ko03450 Non-homologous end-joining 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3. Environmental Information Processing 176 202 180 171 222 174 209 218 186 179 215 214 194 219
3.1 Membrane Transport 119 141 125 114 172 135 159 163 138 131 162 165 148 170
ko02010 ABC transporters 88 91 85 84 119 97 117 127 112 109 132 120 120 141 ko02060 Phosphotransferase system 3 4 3 4 7 3 4 3 4 3 4 4 3 3 ko03070 Bacterial secretion system 28 46 37 26 46 35 38 33 22 19 26 41 25 26
Table S1. Cont.
Relevant KEGG Pathways KEGG ORTHOLOGS
azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
3.2 Signal Transduction 57 61 55 57 50 39 50 55 48 48 53 49 46 49
ko02020 Two-component system 57 61 55 57 50 39 50 55 48 48 53 49 46 49 4. Cellular Processes 38 41 43 43 34 38 40 41 40 40 41 40 40 40
4.2 Cell Motility 38 41 43 43 34 38 40 41 40 40 41 40 40 40
ko02030 Bacterial chemotaxis 13 13 15 15 9 13 15 16 15 15 16 15 15 15 ko02040 Flagellar assembly 25 28 28 28 25 25 25 25 25 25 25 25 25 25
Table S2. Nitrogen metabolism KEGG orthologs.
#K0 Cluster Coding gene product azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
K00260 1951 gdhB glutamate dehydrogenase K00261 4283 glutamate dehydrogenase (NAD(P)+) K00262 21243 gdhA glutamate dehydrogenase
K00265 1033 gltB glutamate synthase (NADPH/NADH) large chain
K00266 1034 gltD glutamate synthase (NADPH/NADH) small chain
K00285 110 dadA D-amino-acid dehydrogenase
K00362 91 nirB nitrite reductase (NAD(P)H) large subunit
K00363 2427 nirD nitrite reductase (NAD(P)H) small subunit [EC:1.7.1.4]
K00366 4938 nirA ferredoxin-nitrite reductase [EC:1.7.7.1]
K00368 2243 nitrite reductase (NO-forming) [EC:1.7.2.1]
K00369 19160 nitrate reductase [EC:1.7.99.4]
Table S2. Cont.
#K0 Cluster Coding gene product azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
K00371 10313 narB/narY nitrate reductase 1, beta subunit [EC:1.7.99.4]
K00372 1063 nasA nitrate reductase catalytic subunit [EC:1.7.99.4]
K00373 10314 narJ nitrate reductase 1, delta subunit [EC:1.7.99.4]
K00374 10315 narI nitrate reductase 1, gamma subunit [EC:1.7.99.4]
K00376 6625 nosR nitrous-oxide reductase [EC:1.7.99.6]
K00459 706 nitronate monooxygenase [EC:1.13.12.16]
K00605 891 gcvT aminomethyltransferase [EC:2.1.2.10] K00926 4431 arcC carbamate kinase [EC:2.7.2.2] K01424 5986 ansA L-asparaginase [EC:3.5.1.1] K01425 1394 glsA glutaminase [EC:3.5.1.2] K01667 19856 tnaA tryptophanase [EC:4.1.99.1] K01455 4215 formamidase [EC:3.5.1.49] K01501 7648 nitrilase [EC:3.5.5.1] K01673 622 cynT carbonic anhydrase [EC:4.2.1.1] K01674 3373 cah carbonic anhydrase [EC:4.2.1.1] K01725 4944 cynS cyanate lyase [EC:4.2.1.104] K01744 265 aspA aspartate ammonia-lyase [EC:4.3.1.1] K01745 200 hutH histidine ammonia-lyase [EC:4.3.1.3] K01758 16459 cystathionine gamma-lyase [EC:4.4.1.1] K01760 34 metC cystathionine beta-lyase [EC:4.4.1.8] K01915 270 glnA glutamine synthetase [EC:6.3.1.2] K01916 3991 nadE NAD+ synthase [EC:6.3.1.5]
Table S2. Cont.
#K0 Cluster Coding gene product azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
K01953 666 asnB asparagine synthase (glutamine-hydrolysing) [EC:6.3.5.4]
K02164 3392 norE nitric-oxide reductase NorE protein [EC:1.7.99.7]
K02305 3393 norC nitric-oxide reductase, cytochrome c-containing subunit II [EC:1.7.99.7]
K02448 3394 norD nitric-oxide reductase NorD protein [EC:1.7.99.7]
K02567 3389 napA periplasmic nitrate reductase NapA [EC:1.7.99.4]
K02586 190 nifD nitrogenase molybdenum-iron protein alpha chain [EC:1.18.6.1]
K02588 307 nifH nitrogenase iron protein NifH [EC:1.18.6.1]
K02591 213 nifK nitrogenase molybdenum-iron protein beta chain [EC:1.18.6.1]
K04561 3394 norB nitric-oxide reductase, cytochrome b-containing subunit I [EC:1.7.99.7]
K04748 2653 norQ nitric-oxide reductase NorQ protein [EC:1.7.99.7]
K04835 16420 methylaspartate ammonia-lyase [EC:4.3.1.2]
K07256 21185 tauY taurine dehydrogenase large subunit [EC:1.4.2.-]
Nitrogenase complex genes * The gray color indicates absence of the gene.
Table S3. Nod protein orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
nodA 2102
nodB 1929
nodC 2101
nodD 104
nodE 66
nodF 3950
nodG 2
nodH 9911
nodI 109
nodJ 2100
nodL 1854
nodM 383
nodN 526
nodO 19055
nodP 404
nodQ 374
nodR 19236
nodS 3695
nodT 418
nodU 5971
nodV 82
nodW 63
nodX 3712
nodY 12393
nodZ 4207
* The gray color indicates absence of the gene.
Table S4. Noe protein orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
noeA 5425
noeB 9915
noeC 2980
noeD 12248
noeE 6845
noeI 5361
noeJ 400
noeK 400
noeL 428
* The gray color indicates absence of the gene.
Table S5. Nol protein orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
nolA 12390
nolB 12304
nolE 9252
nolF 9909
nolG 23
nolK 745
nolL 7064
nolM 12394
nolN 3832
nolO 3832
nolP 17948
nolR 5722
nolT 9214
nolU 6835
Table S5. Cont.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
nolV 6836
nolW 5357
nolX 9043
nolY 12389
nolZ 12388
* The gray color indicates absence of the gene.
Table S6. Twin arginine transporter system protein orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
tatA 10369
tatA 6424
tatA 8875
tatA 4621
tatA 7457
tatA 20553
tatB 4991
tatB 14080
tatB 14102
tatB 8115
tatB 2731
tatB 4770
tatC 2980
* The gray color indicates absence of the gene.
Table S7. Type I secretion protein orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
tolC 1327
hlyD family 51
hlyD 3801
hlyD 2353 nodO 19055
hlyB/aprD/aprE/prtDE system 13
* The gray color indicates absence of the gene.
Table S8. Type II secretion sec orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
secA 1374 secB 1594
secD/F 252 secE 10212 secE 13078 secE 11643 secE 14008 secE 15467 secE 15053 secE 17716 secE 17204 secE 7448 secE 19349 secE 20037 secE 18819 secG 5403 secG 15542
Table S8. Cont.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
secG 15040 secG 4637 secY 1298 yidC 1464 ftsY 1420 ffh 1439
yacJ 1344 * The gray color indicates absence of the gene.
Table S9. Type II secretion gsp orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
gspD 3007 gspE 3382 gspF 9051 gspF 12992 gspF 4258 gspG 3383 gspH 16602 gspH 18602 gspH 3750 gspI 16603 gspI 18601 gspI 13907 gspI 7996 gspJ 16604 gspJ 18600 gspJ 3751
Table S9. Cont.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
gspK 16601 gspK 18603 gspK 3752 gspL 9050 gspL 4259 gspM 4260
* The gray color indicates absence of the gene.
Table S10. Type III secretion nop/ysc/rhc orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
nopL 18019 nopP 4327 nopT 6843 nopJ 17997 nopM 4356
yscC/rhcC 5357 yscJ/rhcJ 4358 yscJ/rhcJ 9214 yscS/rhcS 9045 yscS/rhcS 14734 yscS/rhcS 12305
yscR/rhcR/fliP 371 yscT/rhcT 5358 yscT/rhcT 14735 yscT/rhcT 9218 yscU/rhcU 5359 yscU/rhcU 9219
Table S10. Cont.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
yscVrhcV/flhA ** 373 yscN/rhcN/fliI*** 372
yscQ/rhcQ/fliN 6838 yscQ/rhcQ/fliN 9217
yscL/nolV 6836 yscL/nolV 9216
* The gray color indicates absence of the gene.
Table S11. F-type Type IV secretion protein orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
trbD 2283 trbJ 2105 trbL 1194 trbF 1195 trbI 572
virB1 3079 tIrB2/trbC 5995 tIrB2/trbC 13648 tIrB2/trbC 9347 tIrB2/trbC 5706 tIrB2/trbC 10779
virB3 3365 virB4 9336
virB4/TrbE 1621 virB4/TrbE 647
virB5 3364 virB5 9337
Table S11. Cont.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
virB5 19707 virB6/trbL 3363 virB6/trbL 20231 virB6/trbL 4866
VirB7 18203 VirB7 17844 VirB7 7219
virB8/trbF 2126 virB8/trbF 9339 virB8/trbF 4865
VirB9/TrbG 2296 VirB9/TrbG 5412 VirB9/TrbG 648 VirB10/TrbI 1620 VirB11/TrbB 58
* The gray color indicates absence of the gene.
Table S12. P-type type IV secretion protein orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
cpaA 2527 cpaB 464 cpaC 179 cpaD 779 cpaE 397 cpaF 58 tadB 358 tadC 461
Table S12. Cont.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
pilA 4511 pilA 18209
* The gray color indicates absence of the gene.
Table S13. Type V secretion protein orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
autA 3479 autB 3479 autC 599
* The gray color indicates absence of the gene.
Table S14. Type VI secretion protein orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
impA 7826 impB 3667 impC 3479 impD 2956 impE 7827 impF 18699 impG 3331 impH 3668 impI 18698 impJ 3666 impK 3329 impL 3330 impM 18697 impN 18696
* The gray color indicates absence of the gene. Table S15. Exo exopolysacchride synthesis protein orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
exoA 3887 exoA 103 exoB 130 exoD 5463 exoD 2952 exoF 2720 exoH 18229 exoI 2139 exoI 1865 exoL 4424 exoM 4425
exoM/pssC 4707 exoN 474 exoO 3480
exoP/pssP 357 exoP 1805 exoQ 4423 exoQ 4795 exoR 861 exoS 1469 exoT 9669 exoT 4422 exoU 4482 exoU 3496
exoV/pssM 3083 exoX 9679
Table S15. Cont.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
exoX 9248 exoY1 105 exoY2 520 exoZ1 1768
exoZ2/exoK 4421 * The gray color indicates absence of the gene.
Table S16. Pss exopolysacchride synthesis protein orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
pssA 1160 pssB 615 pssC 4707 pssD 4709 pssE 4710 pssF 4706 pssF 7396 pssG 2557 pssH 2557 pssI 2557 pssJ 5772 pssK 4082 pssL 4705
pssM/exoV 3083 pssN/Wza 678
pssO 4713 pssP/exoP 357
Table S16. Cont.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
pssR 4704 pssS 3579
pssT/Wzy 2644 pssV 2891
Table S17. Fix orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
fixA 1726 fixB 1727 fixC 1728 fixX 1939 fixF 17970 fixJ 63 fixK 420 fixL 82 fixM 676 fixN 350 fixO 351 fixP 352 fixQ 18756 fixQ 18725 fixQ 7676 fixQ 7256 fixQ 12558 fixQ 13950 fixQ 7222 fixQ 16567
Table S17. Cont.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
fixQ 16510 fixQ 10911 fixR 2241 fixG 394 fixH 5105 fixH 2028 fixI 43 fixS 19875 fixS 19241 fixS 17492 fixS 12559 fixS 11400 fixS 13951 fixS 17933 fixS 17625 fixS 16566 fixS 16511 fixS 20466 fixS 21060 fixT 9684 fixU 4485 fixU 5061 fixW 20730
fixABCX operon - involved in transcription regulation under low O2 i.e in bacteroid form within the nodule. fixNOPQ operon - cytochrome cbb3 oxidase. Crucial for oxygen regulation between bacteroid and host plant root cell. fixQ = Cytochrome cbb3 subunit IV. Differs signifcantly in different species hence multiple clusters. fixGHIS operon - believed to be required for construction of cbb3 oxidase from fix NOPQ components
* The gray color indicates absence of the gene.
Table S18. Nif orthologs.
Coding gene Cluster azc bja bbt bra mlo mes ret rec rlg rlt rle rhi smd sme
nifA 30 nifB 1381 nifD 190 nifH 307 nifK 213 nifE 190 nifN 213 nifX 2237 nifL* 168 nifQ 2971 nifR 1362 nifS 346
nifT** 9684 nifT** 4485 nifT** 5061 nifU 1606 nifW 2972 nifZ 2970
Nitrogenase complex. nifE and nifD stuctually homologous to nifN and nifK respectively * nifL - diguanylate cyclase with PAS/PAC sensor only identified as such in rlt. nifL region spans most of the protein. nifL is a negative nif regulator. It is in a cluster shared by all 13 Fix+ genomes entitled “noproteinhit”. All proteins in cluster have various combinations of PAS and CCGF/Diguanylate cyclase domains. ** nifT also know as fixU or fixT * The gray color indicates absence of the gene.