Table 2.
Relevant genes of the accessory genome related to symbiotic interaction
| Orthologous group(s)* | Gene or Protein Name | Strain(s) | Copies | Phenotype*** | Species**** | NodMutID |
|---|---|---|---|---|---|---|
| Microaerophilic gene set | ||||||
| 5488 | fixK-like | Rm1021/BL225C | 4 | Nod+Fix- | B. japonicum USDA110 | 924-5 |
| 5305, 5324, 5377, 5379 | fixNOQP3 | Rm1021/BL225C | 3 | Nod+Fix- | B. japonicum USDA110 | 933-950 |
| 5327, 5300, 5361, 5326, 5378 | norBCDEQ | Rm1021/BL225C | 1 | Nod+- | B. japonicum USDA110 | 921 |
| 5432, 5427, 5508, 5586, 5502, 5567, 5554 | nosRZDFYLX | Rm1021/BL225C | 1 | Nod+Fix+ | B. japonicum USDA110 | 1075 |
| 5498, 5537 | nirKV | Rm1021/BL225C | 1** | Nod+- | B. japonicum USDA110 | 922 |
| 5298, 5394, 5563 | nnrRSU | Rm1021/BL225C | 1** | N2metabolism | S.meliloti JJ1c10 | --- |
| 5441, 5485, 5583 | nrtABC | Rm1021/BL225C | 1** | N2metabolism | S.meliloti Rm1021 | --- |
| 7166 | cycB2 | Rm1021 | 2 | Not known | S. meliloti Rm1021 | --- |
| 5391 | hemN | Rm1021/BL225C | 1 | Not known | S. meliloti JJ1c10 | --- |
| Others | ||||||
| 5422 | Symbiosis-related SDR | Rm1021/BL225C | 1 | Nod+Fix+- | S. meliloti Rm1021 | 1310 |
| 6532 | nwsB | BL225C | 1 | Nod+- | B. japonicum USDA110 | 911, 1015, 1019 |
| 5532, 5338, 5424, 548, 5381, 5346, 5437, 5522 | rhbABCDE, rhtAX, rhrA | Rm1021/BL225C | 1** | Nod+Fix+- | S. meliloti Rm1021 | --- |
| 5832 | acdS | AK83/BL225C | 1 | Nod+- | Several rhizobial species | --- |
| 5635 | fixKweakhomolog | AK83/BL225C | 4 | Nod+Fix- | B.japonicum USDA110 | 924-5 |
| 7649 | nodQ1 | Rm1021/AK83 | 2 | Nod+- | S. meliloti Rm1021 | 104, 119, 134-7, 618, 629 |
| 6799 | fixT3 | Rm1021 | 7 | Not known | S. meliloti Rm1021 | --- |
| 6905 | nodP2 | Rm1021 | 2 | Host | S. meliloti Rm1021 | --- |
| 7041 | fixT2 | Rm1021 | 7 | Nod+Fix+ | S. meliloti Rm1021 | 685 |
| 7042 | fixK2 | Rm1021 | 4 | Nod+Fix- | S. meliloti Rm1021 | 489 |
| 5593 | C P450 | AK83/BL225C | 3 | Nod+Fix+ | B. japonicum USDA110, Rhizobium sp. BR816 | --- |
| 7427 | hupE | AK83 | 1 | Nod+Fix+ | A. caulinodans ORS571 | --- |
| 5770 | hemA homolog | AK83/BL225C | 1 | Nod+Fix+- | B. japonicum USDA110 | --- |
| 6640 | Pcs distant homolog | BL225C | 2 | Host | Several bacterial species | --- |
| 7666 | CTP:phosphocholinecytidylyltransferase | AK83 | 1 | Host | Several bacterial species | --- |
| 7766 | Cadherin-likeprotein | AK83 | 1 | Host | R. leguminosarum bv.viciae | --- |
| 6766 | cgmB | Rm1021 | 1 | Host | S. meliloti Rm1021 | --- |
| 6835 | expR (fragment) | Rm1021 | 1 | Not known | S. meliloti Rm1021 | --- |
| 5551 | Sugar isomerase | Rm1021/BL225C | 1 | Host | S. meliloti Rm1021 | --- |
| 3183 | nodM (AK83) | AK83 | 2 | Host | S. meliloti Rm1021 | --- |
| Not characterized | ||||||
| 6353 | napC/nirT-like | BL225C | 1 | N2metabolism | Several rhizobial species | --- |
| 8184 | glnA-like | AK83 | 9 | N2metabolism | Several rhizobial species | --- |
| 5573 | fixS2 | Rm1021/BL225C | 2 | Not known | S. meliloti Rm1021 | --- |
| 5936 | fixO-like | AK83/BL225C | 2 | Not known | Several rhizobial species | --- |
| 5950 | fixT1-like | AK83/BL225C | 7 | Not known | Several rhizobial species | --- |
| 6498 | fixT-like | BL225C | 7 | Not known | Several rhizobial species | --- |
| 7148 | fixL-related | Rm1021 | 2 | Not known | S. meliloti Rm1021 | --- |
See text and Figure S1 for details of the searching procedure.
* See Table S1 for the accession numbers of the single proteins belonging to each group
** One or more genes are present in more than one copy
*** Host: recognition, communication and invasion of a host plant; Nod: nodulation phenotype; Fix: nitrogen fixation and plant growth promotion phenotype; + positive phenotype; +- slightly reduced phenotype; - absent phenotype
**** Organism in which the function of a specific protein or operon was elucidated