Table 10. Bacterial gene expression in the nodule GI Name Description SLR SD Increased in Rm1021 bacteroids compared to Rm1021 grown in TY medium 14523116 SMa0112 Conserved hypothetical 2.07 0.52 14523122 SMa0121 Hypothetical 5.28 0.60 14523123 SMa0123 Conserved hypothetical 4.09 1.16 14523124 SMa0124 GroEL3 chaperonin 4.50 0.46 14523125 SMa0125 GroES3 chaperonin 4.35 0.26 14523165 SMa0191 Conserved hypothetical 2.32 0.26 14523166 SMa0193 Conserved hypothetical 2.50 0.43 14523189 SMa0229 Conserved hypothetical 1.74 0.21 14523190 SMa0232 Conserved hypothetical 3.10 0.24 14523293 SMa0407 Conserved hypothetical 3.13 0.27 14523315 SMa0453 Similar to Yle from A. tumefaciens 1.92 0.22 14523318 SMa0462 Conserved hypothetical 2.05 0.25 14523325 SMa0471 Conserved hypothetical 1.98 0.42 14523326 SMa0473 Conserved hypothetical 1.17 0.34 14523327 SMa0475 TRm17a transposase 2.51 0.28 14523328 SMa0476 TRm17b transposase 3.71 1.02 14523341 SMa0498 LysR family transcriptional regulator 3.84 0.46 14523384 SMa0576 Leu or Leu/Val/Ile transport binding protein 4.28 0.60 14523385 SMa0579 Adenylate cyclase 1.94 0.71 14523412 SMa0625 Hypothetical 4.29 0.47 14523419 SMa0636 Conserved hypothetical 4.18 1.07 14523433 SMa0661 Conserved hypothetical 3.59 0.92 14523439 SMa0667 Conserved hypothetical 3.57 0.31 14523440 SMa0669 Conserved hypothetical 2.00 0.25 14523445 SMa0677 Glutamate/aspartate transport protein 2.50 0.62 14523453 SMa0689 Conserved hypothetical 3.36 0.33 14523454 SMa0690 Conserved hypothetical 4.57 0.49 14523491 SMa0751 Aromatic-ring hydroxylating dioxygenase 3.86 1.22 14523492 SMa0752 Dioxygenase reductase subunit 4.47 0.79 14523493 SMa0753 Conserved hypothetical 2.93 0.85 14523493 SMa0753 Conserved hypothetical 2.85 0.35 14523494 SMa0754 Hypothetical 3.09 0.98 14523500 SMa0762 FixK2 transcriptional regulator 6.84 0.87 14523501 SMa0763 Conserved hypothetical 8.23 0.72 14523502 SMa0765 FixN2 cytochrome c oxidase polypeptide I 5.88 0.52 14523503 SMa0766 FixO2 cytochrome c oxidase 5.64 0.57 14523504 SMa0767 FixQ2 cbb3-type cytochrome oxidase 6.97 0.23 14523505 SMa0769 FixP2 cytochrome c oxidase 6.87 0.99 14523506 SMa0771 Conserved hypothetical 5.76 0.69 14523507 SMa0772 NodL Nod factor acetyltransferase 5.49 1.33 14523508 SMa0773 NoeA host specific nodulation protein 3.00 0.35 14523509 SMa0774 NoeB host specific nodulation protein 2.20 0.63 14523534 SMa0810 FixU nitrogen fixation protein 5.02 0.85 14523535 SMa0811 FdxN ferredoxin 5.66 0.15 14523536 SMa0814 NifB FeMo cofactor biosynthesis protein 7.09 0.14 14523538 SMa0815 NifA transcriptional activator 6.20 0.32 GI Name Description SLR SD 14523539 SMa0816 FixX ferredoxin-like protein 5.58 0.27 14523540 SMa0817 FixC oxidoreductase 6.35 0.86 14523541 SMa0819 FixB electron transfer flavoprotein alpha chain 6.99 0.42 14523542 SMa0822 FixA electron transfer flavoprotein beta chain 6.93 0.68 14523544 SMa0825 NifH nitrogenase Fe protein 7.54 0.75 14523545 SMa0827 NifD nitrogenase Fe-Mo alpha chain 6.41 0.45 14523547 SMa0829 NifK nitrogenase Fe-Mo beta chain 6.45 0.35 14523548 SMa0830 NifE oxidoreductase 8.02 0.58 14523549 SMa0831 NifX nitrogen fixation protein 4.94 0.62 14523550 SMa0833 Conserved hypothetical 6.97 1.19 14523551 SMa0834 FdxB ferredoxin III 3.96 0.68 14523552 SMa0835 Hypothetical 10.5 kDa ORF, upstream from syrA 3.51 1.46 14523553 SMa0838 SyrA protein involved in EPS production 5.81 0.62 14523556 SMa0846 Conserved hypothetical 1.97 0.61 14523557 SMa0848 Hypothetical, upstream from syrM 2.21 0.30 14523558 SMa0849 SyrM transcriptional regulator 4.25 1.36 14523575 SMa0872 Hypothetical (ORF 110) 1.74 0.32 14523576 SMa0873 NifN Nitrogenase Fe-Mo cofactor biosynthesis protein 1.61 0.46 14523633 SMa0981 NtrR2 transcriptional regulator 1.79 0.15 14523634 SMa0983 Hypothetical 2.64 0.26 14523635 SMa0985 LysR-family transcriptional regulator 3.01 0.42 14523641 SMa0997 Transposase fragment 1.96 0.46 14523687 SMa1073 TRm23b IS ATP-binding protein 3.90 1.65 14523692 SMa1079 TspO tryptophan rich sensory protein 2.04 0.54 14523694 SMa1082 Conserved hypothetical 2.12 0.29 14523704 SMa1096 Conserved hypothetical 2.16 0.32 14523707 SMa1100 Conserved hypothetical 2.57 0.35 14523715 SMa1118 HspC2 heat shock protein 3.03 0.91 14523719 SMa1126 Conserved hypothetical 2.27 0.25 14523720 SMa1128 DegP4 protease 2.64 0.79 14523723 SMa1132 Hypothetical 6.99 1.16 14523724 SMa1134 Hypothetical 5.23 0.53 14523725 SMa1136 Conserved hypothetical 4.70 0.45 14523728 SMa1141 Fnr/Crp family transcriptional regulator 3.01 0.45 14523731 SMa1147 Conserved hypothetical 2.41 0.71 14523736 SMa1154 Conserved hypothetical 2.23 0.75 14523748 SMa1169 Conserved hypothetical 1.74 0.55 14523770 SMa1201 Conserved hypothetical 2.38 0.52 14523771 SMa1207 FixK-like regulator 3.51 1.40 14523772 SMa1208 FixS1 nitrogen fixation protein 5.33 0.36 14523773 SMa1209 FixI1 copper transport ATPase 2.75 0.34 14523774 SMa1210 FixH nitrogen fixation protein 4.64 0.28 14523775 SMa1211 FixG iron sulfur membrane protein 5.55 0.61 14523777 SMa1213 FixP1 di-heme cytochrome c 6.36 0.21 14523778 SMa1214 FixQ1 cbb3-type cytochrome oxidase 6.02 0.53 14523779 SMa1216 FixO1 c-type cytochrome 5.53 0.64 14523780 SMa1220 FixN1 Heme b / copper cytochrome c oxidase subunit 6.08 0.93 14523781 SMa1223 FixM flavoprotein oxidoreductase 7.85 0.46 14523786 SMa1231 Conserved hypothetical 3.02 0.79 14523849 SMa1334 Conserved hypothetical 2.80 0.76 14523852 SMa1339 ABC transporter 2.01 0.18 14523920 SMa1455 Conserved hypothetical 2.30 0.30 GI Name Description SLR SD 14523921 SMa1456 Conserved hypothetical 1.97 0.28 14523953 SMa1515 Hypothetical 1.51 0.20 14524122 SMa1770 Conserved hypothetical 1.63 0.44 14524135 SMa1797 Hypothetical 3.38 0.41 14524201 SMa1910 Conserved hypothetical 4.16 1.17 14524205 SMa1918 Conserved hypothetical 2.30 0.81 14524207 SMa1921 Hypothetical 2.41 0.65 14524208 SMa1924 Conserved hypothetical 1.88 0.32 14524256 SMa2009 Conserved hypothetical 5.38 0.93 14524257 SMa2011 Hypothetical 3.69 0.21 14524281 SMa2055 Conserved hypothetical 2.38 0.26 14524340 SMa2167 Conserved hypothetical 1.45 0.20 14524360 SMa2215 GntR-family transcriptional regulator 3.23 0.14 14524386 SMa2263 Hypothetical 2.02 0.29 14524391 SMa2273 Hypothetical 2.66 0.57 14524392 SMa2275 Conserved hypothetical 5.06 1.20 15139922 SMb20047 Hypothetical 1.71 0.37 15139923 SMb20048 Transcriptional regulator 2.06 0.46 15139924 SMb20049 FusA2 elongation factor G 2.19 0.42 15139938 SMb20066 Hypothetical 1.27 0.47 15139974 SMb20102 Acetoin catabolism regulator 1.58 0.17 15139990 SMb20118 Conserved hypothetical 1.30 0.46 15140033 SMb20161 Hypothetical 2.24 1.08 15140094 SMb20231 ABC transporter, sugar 2.39 0.55 15140095 SMb20232 ABC transporter 2.02 1.15 15140117 SMb20255 Conserved hypothetical 2.10 0.23 15140190 SMb20331 Conserved hypothetical 2.86 0.36 15140199 SMb20340 Conserved hypothetical 1.60 0.36 15140214 SMb20355 Hypothetical 2.84 1.03 15140224 SMb20365 ABC transporter, iron 2.62 1.38 15140320 SMb20465 Conserved hypothetical 2.35 0.31 15140339 SMb20484 ABC transporter, sugar 3.30 0.63 15140363 SMb20508 ABC transporter, sugar 2.28 0.29 15140369 SMb20515 Chemotaxis methyltransferase 1.58 0.17 15140370 SMb20516 Response regulator 2.44 0.55 15140374 SMb20520 Conserved hypothetical 4.20 0.45 15140375 SMb20521 Conserved hypothetical 3.38 0.40 15140376 SMb20522 Conserved hypothetical 2.97 0.51 15140383 SMb20531 RpoE RNA polymerase ECF sigma factor 1.73 0.39 15140391 SMb20539 CyaF6 adenylate cyclase 3.52 1.34 15140407 SMb20544 ISRm14 protein 3.08 0.35 15141392 SMb20592 RpoE RNA polymerase sigma factor 4.77 0.35 15141394 SMb20594 AmcY amicyanin precursor 3.49 0.14 15141415 SMb20615 ThiC thiamine biosynthesis protein 2.09 0.36 15141416 SMb20616 ThiO thiamine biosynthesis oxidoreductase 1.48 0.45 15141242 SMb20647 Conserved hypothetical 2.31 0.71 15141259 SMb20665 ISRm17 partial transposase 2.16 0.20 15141267 SMb20673 ABC transporter 2.77 1.19 15141312 SMb20717 LacI-family transcriptional regulator 2.18 0.63 15140443 SMb20818 MocD hydrocarbon oxygenase 3.59 0.47 15140444 SMb20819 MocE ferredoxin of the Rieseke type 4.48 0.39 15140445 SMb20820 MocF ferredoxin reductase 5.56 1.00 GI Name Description SLR SD 15140446 SMb20821 ATP/GTP-binding hydroxymethyltransferase 3.62 0.89 15140452 SMb20827 Transposase 2.82 0.83 15140465 SMb20837 Conserved hypothetical, transmembrane 1.93 1.17 15140468 SMb20840 Conserved hypothetical 2.63 0.25 15140471 SMb20843 AlgI involved in acetylating a cell surface saccharide 2.12 0.18 15141047 SMb20866 Conserved hypothetical 3.24 0.59 15141089 SMb20906 Hypothetical 2.46 0.51 15141100 SMb20914 Conserved hypothetical 2.19 0.67 15140956 SMb20947 ExoX posttranscriptional repressor 2.06 0.26 15140964 SMb20953 Conserved hypothetical, exported 4.39 0.45 15140501 SMb21044 ATP-dependent DNA ligase 3.86 0.91 15140582 SMb21118 Hypothetical 2.46 0.78 15140764 SMb21212 Conserved hypothetical 1.57 0.29 15140625 SMb21236 ATP/GTP-binding protein 1.56 0.43 15140683 SMb21294 Hsp20-family small heat shock protein 2.74 0.83 15140684 SMb21295 Hsp20-family small heat shock protein 2.44 0.73 15140689 SMb21300 DeoC deoxyribose-phosphate aldolase 1.78 0.31 15140690 SMb21301 Aldehyde dehydrogenase 1.48 0.26 15140795 SMb21333 Hypothetical 2.07 0.43 15140807 SMb21345 ABC transporter, sugar uptake 2.07 0.21 15141112 SMb21399 Conserved hypothetical 3.02 0.29 15141114 SMb21400 Conserved hypothetical 3.32 0.64 15141123 SMb21409 Hypothetical 3.32 0.20 15141158 SMb21442 Conserved hypothetical 3.12 0.27 15141159 SMb21443 Conserved hypothetical 2.04 0.15 15141161 SMb21445 DNA topoisomerase I 5.09 0.34