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Supplementary Table 1 (JB00889-05 Revised)

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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
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  • WO 2017/083351 Al 18 May 2017 (18.05.2017) P O P C T

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    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2017/083351 Al 18 May 2017 (18.05.2017) P O P C T (51) International Patent Classification: MCAVOY, Bonnie D.; 110 Canal Street, Lowell, Mas- C12N 1/20 (2006.01) A01N 41/08 (2006.01) sachusetts 01854 (US). C12N 1/21 (2006.01) C07C 403/24 (2006.01) (74) Agent: JACOBSON, Jill A.; FisherBroyles, LLP, 2784 C12N 15/75 (2006.01) A23L 33/175 (2016.01) Homestead Rd. #321, Santa Clara, California 9505 1 (US). A23K 10/10 (2016.01) A23L 5/44 (2016.01) (81) Designated States (unless otherwise indicated, for every (21) International Application Number: kind of national protection available): AE, AG, AL, AM, PCT/US20 16/06 1081 AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (22) International Filing Date: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, ' November 2016 (09.1 1.2016) DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (25) Filing Language: English KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (26) Publication Language: English MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (30) Priority Data: SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, 62/252,971 ' November 2015 (09.