Supplementary Table 1 Transcriptome profiles of Rhodopseudomonas palustris strains Cells grown in N-fixing mudium (N-fixing conditions) were compared with cells grown in the same medium supplemented with ammonium sulfate (non-N-fixing conditio Remark 1 Profile was determined by 3 comparative experiments and 2 calibration experiments, and two slides were used in each experiment (10 slides per profile) Remark 2 Empty cells indicate that data were not obtained due to the low signal intensities Remark 3 Definition of gene expression change Higher in N-fixing conditions: expression ratio (N-fixing conditions/non-N-fixing conditions) is greater than or equal to 2 AND score is less than 0.025 (at least 95% confident that the expresssion ratio of N-fixing conditions/non-N-fixing conditions is positive, i.e., higher in N-fixing conditions) Lower in N-fixing conditions: expression ratio (N-fixing conditions/non-N-fixing conditions) is less than or equal to 0.5 AND scores is greater than 0.975 (at least 95% confident that the expresssion ratio of N-fixing conditions/non-N-fixing conditions is negative, i.e., lower in N-fixing conditions) Remark 4 Mo strain (CGA753), V strain (CGA766), and Fe strain (CGA755) refer to Mo nitrogenase only strain, V nitrogenase only strain, and Fe nitrogenase only strain, respectively Remark 5 Plus V indicates that 10 µM V was added to the growth medium Col# 1 RPA# Col# 2 The average expression ratio (N-fixing conditions/non-N-fixing conditions) based on (maximum) 12 comparative experimental data points Red: average expression ratio is greater than or equal to 2 (greater than or equal to 2-fold higher in N-fixing conditionand Blue: average expression ratio is less than or equal to 0.5 (greater than or equal to 2-fold lower in N-fixing conditio Col# 3 Score [the probability of logarithmic ratio (N-fixing conditions/non-N-fixing conditions) of expression level below 0] determined by a Markov chain Monte Carlo simulation Red: score is less than 0.025 (the expression ratio is positive, i.e., high in N-fixing conditionand Blue: score is greater than 0.975 (the expression ratio is negative, i.e., low in N-fixing conditions Col# 4 Annotation Col# 1 Col# 2 Col# 3 Col# 2 Col# 3 Col# 2 Col# 3 Col# 2 Col# 3 Col# 2 Col# 3 Col# 4 Wild-type strain Wild-type strain Mo strain V strain Fe strain (plus V) (plus V) (CGA009) (CGA009) (CGA753) (CGA766) (CGA755) RPA# W AvRt W Sco WV AvRt WV Sco Mo AvRt Mo Sco V AvRt V Sco Fe AvRt Fe Sco Annotation RPA0001 0.665963 0.995 0.66581 0.9995 0.535337 0.9995 0.582471 0.997 0.648473 0.9685 dnaA chromosomal replication initiator protein DnaA 679:2097 forward MW:52624 RPA0002 0.832078 0.945 0.713654 0.999 0.750162 0.991 0.632156 0.999 0.700926 0.9985 dnaN DNA polymerase III beta subunit 2332:3450 forward MW:40401 RPA0003 recF putative RecF protein 3667:4833 forward MW:41676 RPA0004 0.589961 1 0.627573 1 0.876581 0.9285 0.546938 0.998 0.704026 0.991 gyrB DNA gyrase subunit B 5050:7491 forward MW:89311 RPA0005 0.948484 0.736 1.012589 0.448 0.905783 0.853 1.185123 0.0515 2.079792 0.002 hpd 4-hydroxyphenylpyruvate dioxygenase 7673:8791 reverse MW:40713 RPA0006 0.660193 0.987 0.620895 0.9975 0.767535 0.9625 0.990005 0.5265 0.873999 0.9175 CDS transcriptional regulator, AsnC family 8917:9396 forward MW:17592 RPA0007 1.004884 0.467 1.013173 0.462 1.086041 0.19 0.788753 0.9625 0.801843 0.965 CDS putative signal transduction histidine kinase with PAS/PAC domains 9442:10893 reverse MW:51220 RPA0008 0.972158 0.6615 1.094975 0.147 1.083926 0.193 1.013045 0.457 0.969496 0.6055 kaiB circadian clock protein 10890:11174 reverse MW:10217 RPA0009 1.157415 0.1305 1.104502 0.1365 0.883592 0.8835 0.886024 0.8 1.021125 0.4 kaiC circadian clock protein 11184:12875 reverse MW:61906 RPA0010 0.756573 0.93 0.542423 0.9885 0.642433 0.978 0.770893 0.7905 0.640031 0.98 CDS possible glutamate uptake transcriptional regulator, AsnC family 13269:13778 reverse MW:18704 RPA0011 1.538605 0.004 1.250146 0.0475 1.37407 0.011 1.331754 0.071 1.078848 0.3385 CDS conserved hypothetical protein 14266:14514 reverse MW:9325 RPA0012 1.435202 0.048 1.511813 0.0035 1.494955 0.012 1.798991 0.004 1.418852 0.0105 rdxS, fixS possible fixS 14516:14701 reverse MW:6468 RPA0013 1.215864 0.027 1.183082 0.0665 1.195945 0.101 1.239875 0.0345 0.788519 0.9025 rdxI, fixI putative cation (heavy metal) transporting ATPase 14692:16890 reverse MW:77870 RPA0014 1.229704 0.027 1.58493 0.005 1.21545 0.125 1.525197 0.0385 1.034979 0.385 rdxH, fixH conserved hypothetical protein 16925:17428 reverse MW:18109 RPA0015 1.476543 0.003 1.763539 0.001 1.377831 0.022 1.835532 0.0125 1.543146 0.027 fixG, rdxB 4Fe-4S ferredoxin, iron-sulfur binding domain 17445:18902 reverse MW:54555 RPA0016 1.995855 0.0005 1.991599 0 1.948835 0.001 2.142437 0.003 1.549919 0.0035 ccoP, fixP cytochrome-c oxidase fixP chain 19019:19900 reverse MW:31591 RPA0017 1.474059 0.014 1.710393 0.0015 1.54257 0.006 1.414015 0.04 1.094925 0.197 ccoQ, fixQ cytochrome oxidase subunit, small membrane protein 19908:20072 reverse MW:6267 RPA0018 2.109964 0 2.205291 0.0015 2.23222 0.0015 2.169297 0.0045 1.441704 0.0325 ccoO, fixO cytochrome-c oxidase fixO chain 20082:20816 reverse MW:27263 RPA0019 1.818109 0.002 1.738453 0.001 1.941932 0.006 1.832428 0.005 1.333838 0.005 ccoN, fixN cytochrome-c oxidase fixN chain, heme and copper binding subunit 20829:22475 reverse MW:61588 RPA0020 0.729271 0.9785 0.799716 0.968 0.92995 0.7345 0.764698 0.9105 0.708331 0.9925 panE1 Ketopantoate reductase ApbA/PanE 22786:23706 reverse MW:32340 RPA0021 0.823356 0.896 0.753434 0.9755 0.905621 0.7475 0.799699 0.886 0.802977 0.912 CDS possible short chain dehydrogenase 23779:24516 reverse MW:26621 RPA0022 CDS DSBA oxidoreductase 24637:25239 reverse MW:22293 RPA0023 1.016277 0.413 0.891777 0.8805 0.956305 0.701 0.832687 0.9565 0.926943 0.6955 gstA3 possible glutathione transferase 25362:26123 forward MW:28571 RPA0024 0.938735 0.7555 1.132245 0.062 0.912631 0.7995 1.017442 0.4495 1.023153 0.4225 CDS Short-chain dehydrogenase/reductase SDR 26235:27110 reverse MW:30727 RPA0025 1.071125 0.313 0.804989 0.9825 0.978916 0.614 0.794189 0.9775 0.837225 0.959 ggt1 gamma-glutamyltranspeptidase 27385:29118 reverse MW:60414 RPA0026 0.780263 0.993 0.72297 0.997 0.836173 0.9415 0.494706 0.9985 0.682774 0.9815 CDS Major Facilitator Superfamily (MFS) transporter 29224:30621 forward MW:49109 RPA0027 0.626608 0.974 0.539779 0.9995 0.565933 1 0.457924 0.9975 0.51349 0.999 aroG1 2-dehydro-3-deoxyphosphoheptonate aldolase 30837:31931 forward MW:38504 RPA0028 0.825066 0.9675 0.875109 0.914 0.58885 1 0.836575 0.9275 1.121169 0.266 purH bifunctional purine biosynthesis protein 31989:33581 reverse MW:55969 RPA0029 0.845467 0.9365 0.768642 0.996 0.811002 0.983 0.641503 0.999 0.83785 0.962 CDS conserved hypothetical protein 33767:35653 reverse MW:69043 RPA0030 0.574225 0.996 0.608447 0.9805 0.83391 0.9625 0.429529 0.999 0.575819 0.9985 CDS Bacterial Sun/eukaryotic nucleolar Nop1/Nop2 35820:37172 reverse MW:48051 RPA0031 0.720167 0.92 0.825327 0.7185 0.831532 0.8675 0.618629 0.9795 CDS conserved hypothetical protein 37325:37543 forward MW:7774 RPA0032 0.894084 0.841 1.033433 0.437 0.903145 0.8715 0.809264 0.8275 0.846422 0.946 CDS possible Staphylococcal nuclease homologues 37629:38204 forward MW:21361 RPA0033 1.241882 0.1865 0.77885 0.931 1.215192 0.037 0.945283 0.627 0.831397 0.878 CDS conserved hypothetical protein 38208:39092 reverse MW:32310 RPA0034 0.507185 1 0.39952 0.9995 0.542011 0.9995 0.338681 0.9995 0.306156 1 CDS possible flavin containing amine oxidase 39440:40897 forward MW:50840 RPA0035 0.606665 0.996 0.59874 0.9975 0.613304 1 0.657503 0.975 0.617981 0.908 pheT putative phenylalanine-tRNA ligase beta chain 40904:43315 reverse MW:85210 RPA0036 0.702134 0.981 0.813587 0.92 0.727408 0.9975 0.589327 0.9975 0.626656 0.942 CDS conserved unknown protein 43460:43939 reverse MW:17908 RPA0037 0.595524 0.9885 0.873054 0.9605 0.576278 0.9995 0.702 0.995 0.962009 0.6255 pheS phenylalanyl-tRNA synthetase, alpha-subunit 44200:45282 reverse MW:40115 RPA0038 1.078039 0.3495 1.017722 0.388 0.745839 0.987 0.846019 0.961 0.941254 0.694 rplT ribosomal protein L20 45426:45785 reverse MW:13300 RPA0039 0.917195 0.8105 1.179395 0.047 0.775479 0.985 1.0775 0.234 1.182074 0.0665 rpmI 50S ribosomal protein L35 45869:46069 reverse MW:7547 RPA0040 0.933369 0.6405 1.48114 0.016 1.220435 0.069 1.313212 0.0755 1.062968 0.299 infC translation initiation factor IF-3 46403:46981 reverse MW:21922 RPA0041 0.80406 0.96 0.681026 0.9775 0.678227 0.988 0.612673 0.9825 0.760538 0.991 CDS conserved unknown protein 47263:48048 forward MW:28350 RPA0042 1.023413 0.425 0.870792 0.841 0.919883 0.764 1.367083 0.06 1.290854 0.0575 CDS possible iron-sulfur cluster binding protein 48211:49323 reverse MW:40319 RPA0043 0.862491 0.925 1.049005 0.3565 0.81973 0.9355 0.978042 0.5835 0.979389 0.6025 CDS possible glutathione S-transferase 49368:50060 reverse MW:26063 RPA0044 0.768773 0.9845 1.020344 0.407 0.656237 0.9985 0.644429 0.9945 0.803942 0.905 bacA bacitracin resistance protein 50260:51066 forward MW:29341 RPA0045 0.707499 1 0.699705 0.9935 0.823524 0.9745 0.839708 0.9435 0.813824 0.9885 CDS putative NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 51116:52081 reverse MW:33871 RPA0046 0.601368 0.9915 0.724339 0.9965 0.682884 0.998 0.620636 0.9995 0.707856 0.9875 CDS 3'-5' exonuclease 52495:53109 forward MW:22696 RPA0047 0.673268 0.991 0.777338 0.995 0.743545 0.9745 0.598133 0.9945 0.72011 0.997 CDS conserved hypothetical protein 53339:54079 forward MW:26825 RPA0048 0.659016 0.985 0.777336