Supplemental Table S1. H.influenzae hyper-transcribed genes (>100 SNR) in E.coli
ID / Name / Description / Start / SNR / E.coli ortholog / SNRHI0001 / gapdH / glyceraldehyde-3-phosphate dehydrogenase / 13 / 633.11 / EG10367 / 123.88
HI0035 / - / conserved hypothetical protein / 36,694 / 172.25 / EG11536 / 25.14
HI0052 / - / TRAP transporter solute receptors DctP component / 52,689 / 207.60 / - / -
HI0053 / - / zinc-type alcohol dehydrogenase / 53,755 / 606.64 / G6838 / 1.42
HI0073 / - / nucleotidyltransferases putative / 79,506 / 130.97 / - / -
HI0097 / hitA / iron(III) ABC transporters periplasmic-binding protein / 104,475 / 153.55 / - / -
HI0504 / rbsB / D-ribose ABC transporters periplasmic-binding protein / 520,961 / 108.54 / EG10815 / 332.07
HI0534 / aspA / aspartate ammonia-lyase / 558,788 / 528.94 / EG10095 / 137.96
HI0546 / priB / primosomal replication protein N / 568,520 / 124.01 / EG10764 / 84.29
HI0600 / recA / recA protein / 621,735 / 196.57 / EG10823 / 14.72
HI0601 / sxy / DNA transformation protein / 622,884 / 290.34 / G6494 / 5.65
HI0740 / yhxB / phosphomannomutase / 799,963 / 208.85 / - / -
HI0834 / frdB / fumarate reductases iron-sulfur protein / 883,204 / 235.05 / EG10331 / 32.01
HI0835 / frdA / fumarate reductases flavoprotein subunit / 883,896 / 260.61 / EG10330 / 157.15
HI0880 / rpL21 / ribosomal protein L21 / 932,384 / 100.43 / EG50001 / 7.34
HI0946.1 / - / L-2s4-diaminobutyrate decarboxylase / 1,006,759 / 340.87 / - / -
HI0947 / vapC / virulence associated protein C / 1,008,218 / 318.83 / - / -
HI1010 / - / 3-hydroxyisobutyrate dehydrogenases putative / 1,074,445 / 151.79 / G7417 / 1.58
HI1011 / - / conserved hypothetical protein / 1,075,585 / 271.90 / G7418 / 1.49
HI1012 / - / sugar isomerases putative / 1,076,595 / 215.08 / G7419 / 2.17
HI1014 / - / conserved hypothetical protein / 1,078,062 / 135.45 / - / -
HI1015 / gntP / gluconate permease / 1,079,177 / 222.94 / EG12380 / 2.37
HI1031 / - / conserved hypothetical protein / 1,096,550 / 147.28 / EG12279 / 1.67
HI1077.1 / - / hypothetical protein / 1,144,522 / 439.55 / - / -
HI1124 / oppA / oligopeptide ABC transporters periplasmic-binding protein / 1,190,576 / 195.15 / EG10674 / 21.53
HI1125 / talB / transaldolase B / 1,192,232 / 128.73 / EG11556 / 100.46
HI1126.1 / - / hypothetical protein / 1,194,440 / 125.12 / - / -
HI1210 / mdh / malate dehydrogenase / 1,276,572 / 582.69 / EG10576 / 149.94
HI1245 / - / malate oxidoreductases putative / 1,318,116 / 216.38 / G7293 / 31.09
HI1476 / - / transcriptional regulatory protein / 1,559,968 / 216.49 / - / -
HI1480 / - / hypothetical protein / 1,563,606 / 121.43 / - / -
HI1492 / - / hypothetical protein / 1,569,316 / 212.48 / - / -
HI1584 / ilvH / acetolactate synthase III small subunit / 1,651,481 / 207.50 / EG10499 / 0.84
HI1585 / ilvI / acetolactate synthase III large subunit / 1,652,198 / 125.53 / EG10494 / 7.73
HI1659 / nrdA / ribonucleoside-diphosphate reductases alpha chain / 1,725,100 / 144.26 / EG10660 / 12.45
HI1661 / sucB / 2-oxoglutarate dehydrogenase E2 components dihydrolipoamide succinyltransferase / 1,728,500 / 253.16 / EG10980 / 74.21
HI1739.1 / lctD / L-lactate dehydrogenase / 1,822,497 / 204.52 / - / -
Supplemental Table S2. Summary of E.coli genes differentially transcribed +/- 2-fold compared to native E.coli values, and observed in 50% or more of the clone propagation experiments.
EG10998 / thrA / aspartate kinase I / homoserine dehydrogenase I / 631 / 0.35 / 0.39 / 0.33
EG10999 / thrB / homoserine kinase / 2,801 / 0.45 / 0.37 / 0.34
EG11078 / nhaR / NhaR-Na+ transcriptional activator / 18,738 / 2.06 / 2.25 / 2.10
EG10344 / ftsW / cell division; membrane protein involved in shape determination / 98,822 / 0.50 / 0.47 / 0.48 / 0.33
EG10619 / murC / UDP-N-acetylmuramate-alanine ligase / 100,765 / 0.43 / 0.48 / 0.44
EG12314 / yacG / conserved hypothetical protein with a zinc finger / 111,699 / 2.91 / 2.64 / 3.12 / 2.80
EG11748 / yadD / hypothetical protein / 147,016 / 0.48 / 0.45 / 0.46
EG10302 / fhuA / outer membrane protein receptor for ferrichromes colicin Ms and phages T1s T5s and phi80 / 167,521 / 2.40 / 2.56 / 2.82 / 4.01
EG12335 / cdaR / SdaR transcriptional regulator / 182,445 / 0.32 / 0.25 / 0.23
EG10770 / proS / prolyl-tRNA synthetase / 217,154 / 2.50 / 4.68 / 2.59 / 2.42
G6108 / yafK / conserved protein; in enteroaggregative E. colis YafK is required for development of biofilms / 245,111 / 3.43 / 3.91 / 2.99 / 3.37
G6142 / yagG / YagG GPH Transporter / 284,619 / 0.31 / 0.40 / 0.19
G6178 / ykgG / putative transporter / 323,066 / 2.36 / 2.20 / 2.21
EG10727 / phoA / alkaline phosphatase / 400,977 / 0.45 / 0.49 / 0.49 / 0.37
EG10812 / queA / S-adenosylmethionine:tRNA ribosyltransferase-isomerase / 424,235 / 2.07 / 3.43 / 2.17 / 2.83 / 2.59
EG10439 / hha / haemolysin expression modulating protein / 479,315 / 0.23 / 0.30 / 0.27
EG12429 / ybaJ / conserved hypothetical protein / 479,569 / 0.16 / 0.35 / 0.38 / 0.14
EG10032 / adk / adenylate kinase / 496,425 / 3.14 / 2.84 / 2.18 / 2.80
G6261 / ybaS / putative glutaminase / 510,885 / 0.42 / 0.28 / 0.29 / 0.17
G6262 / ybaT / YbaT APC transporter / 511,815 / 0.40 / 0.46 / 0.26
EG11740 / nfrA / bacteriophage N4 receptors outer membrane protein / 587,207 / 0.44 / 0.37 / 0.38 / 0.37
G6326 / ybdK / conserved hypothetical protein / 605,824 / 0.42 / 0.25 / 0.24 / 0.24
EG10167 / cstA / peptide transporter induced by carbon starvation / 629,122 / 0.23 / 0.39 / 0.32
EG11384 / ahpC / AhpC component / 638,288 / 0.50 / 0.38 / 0.25
EG10856 / rna / RNase Is cleaves phosphodiester bond between any two nucleotides / 643,469 / 0.38 / 0.48 / 0.44
G6338 / citT / CitT citrate DASS Transporter / 644,429 / 0.43 / 0.48 / 0.43
EG12209 / crcB / protein involved in resistance to camphor-induced chromosome decondensation / 656,817 / 0.36 / 0.49 / 0.47
EG11592 / ybeD / conserved hypothetical protein / 661,603 / 0.45 / 0.26 / 0.37 / 0.25
EG12851 / ybeL / conserved hypothetical protein / 674,347 / 0.32 / 0.38 / 0.43
G6351 / ybeQ / conserved hypothetical protein / 674,891 / 0.27 / 0.41 / 0.32 / 0.29
G6356 / djlC / Hsc56; a DnaJ-like protein that activates ATPase activity of Hsc62 / 679,469 / 0.32 / 0.44 / 0.35
G6358 / rihA / ribonucleoside hydrolase 1 (pyrimidine-specific) / 682,802 / 0.38 / 0.38 / 0.30
EG12663 / gltL / glutamate ABC transporter / 683,753 / 0.16 / 0.24 / 0.33
EG12662 / gltK / glutamate ABC transporter / 684,534 / 0.14 / 0.22 / 0.25 / 0.45
EG12661 / gltJ / glutamate ABC transporter / 685,171 / 0.12 / 0.21 / 0.33
G6359 / gltI / putative periplasmic binding transport protein / 686,153 / 0.23 / 0.27 / 0.33 / 0.36
EG10979 / sucA / subunit of E1(0) component of 2-oxoglutarate dehydrogenase / 757,994 / 0.40 / 0.28 / 0.47 / 0.47
EG10981 / sucC / succinyl-CoA synthetases beta subunit / 762,465 / 0.38 / 0.44 / 0.40
EG10982 / sucD / succinyl-CoA synthetases alpha subunit / 763,445 / 0.30 / 0.34 / 0.35
EG11239 / ybhA / putative phosphatase / 796,940 / 2.27 / 2.26 / 2.56 / 2.12
G6406 / ybhO / cardiolipin synthase 2 / 821,723 / 0.49 / 0.36 / 0.49 / 0.49
EG11235 / rhlE / DEAD-box-containing ATP-dependent RNA helicase family member / 830,352 / 2.11 / 2.10 / 2.30 / 3.00
EG12421 / ybiI / conserved hypothetical protein / 837,416 / 0.45 / 0.48 / 0.49
G6442 / ybjI / conserved protein with a phophatase-like domain / 884,542 / 2.02 / 2.46 / 2.28
EG11624 / artP / arginine ABC transporter / 902,231 / 0.47 / 0.49 / 0.46
G6460 / somA / putative enzyme / 917,680 / 3.03 / 2.82 / 2.59 / 2.24
EG11253 / ycbB / putative amidase / 980,272 / 0.15 / 0.32 / 0.37 / 0.34
G6474 / ycbK / conserved hypothetical protein / 982,376 / 2.13 / 2.00 / 2.06
EG10671 / ompF / outer membrane porin OmpF / 985,119 / 2.96 / 6.31 / 11.32 / 8.87
G6486 / ycbW / conserved hypothetical protein / 1,005,139 / 3.28 / 5.99 / 2.38 / 2.62 / 2.61 / 2.34
G6487 / ycbX / putative Fe-S protein / 1,005,718 / 2.27 / 2.60 / 3.38
EG10468 / hyaA / hydrogenase Is HyaA subunit / 1,031,510 / 0.23 / 0.45 / 0.27 / 0.18
EG10469 / hyaB / hydrogenase Is HyaB subunit / 1,032,540 / 0.23 / 0.31 / 0.20
EG10470 / hyaC / hydrogenase Is b-type cytochrome subunit / 1,034,478 / 0.35 / 0.36 / 0.17
EG10471 / hyaD / processing of HyaA and HyaB proteins / 1,035,102 / 0.34 / 0.32 / 0.20
EG10472 / hyaE / processing of HyaA and HyaB proteinss chaperone / 1,035,687 / 0.39 / 0.32 / 0.22
G6516 / ycdF / hypothetical protein / 1,067,189 / 0.19 / 0.05 / 0.07 / 0.06
EG10801 / putA / PutA transcriptional regulator / 1,074,180 / 0.30 / 0.29 / 0.17
EG11734 / phoH / PhoB-dependents ATP-binding pho regulon component; may be helicase; induced by P starvation / 1,084,257 / 2.17 / 2.27 / 4.01
G357 / flgA / flagellar biosynthesis; assembly of basal-body periplasmic P ring / 1,129,438 / 7.18 / 15.49 / 5.57
G358 / flgB / flagellar biosynthesiss cell-proximal portion of basal-body rod / 1,130,320 / 16.09 / 33.89 / 12.53 / 2.46
G359 / flgC / flagellar biosynthesiss cell-proximal portion of basal-body rod / 1,130,840 / 43.07 / 76.53 / 27.35 / 6.42
G360 / flgD / flagellar biosynthesiss initiation of hook assembly / 1,131,131 / 13.07 / 27.85 / 9.12 / 3.31
G361 / flgE / flagellar biosynthesiss hook protein / 1,131,797 / 20.29 / 49.86 / 20.89 / 3.94
G362 / flgF / flagellar biosynthesiss cell-proximal portion of basal-body rod / 1,133,025 / 4.86 / 11.99 / 4.60 / 2.13
G363 / flgG / flagellar biosynthesiss cell-distal portion of basal-body rod / 1,133,953 / 7.57 / 17.54 / 6.22
G364 / flgH / flagellar biosynthesiss basal-body outer-membrane L (lipopolysaccharide layer) ring protein / 1,134,912 / 2.19 / 5.36 / 3.01
G365 / flgI / homolog of Salmonella P-ring of flagella basal body / 1,135,558 / 2.22 / 4.66 / 2.89
EG11118 / rluC / 23S rRNA pseudouridine synthase / 1,144,205 / 2.43 / 2.63 / 3.47
G6612 / b1172 / conserved hypothetical protein / 1,221,869 / 4.45 / 4.08 / 3.34
G6619 / hlyE / hemolysin E / 1,229,004 / 0.28 / 0.35 / 0.31 / 0.21
EG10638 / narG / nitrate reductase A / 1,279,491 / 0.21 / 0.49 / 0.34 / 0.21
EG10640 / narI / nitrate reductase A / 1,285,087 / 0.49 / 0.44 / 0.47 / 0.43
EG10457 / hns / H-NS transcriptional dual regulator / 1,291,819 / 2.66 / 2.53 / 2.72
EG10674 / oppA / oligopeptide ABC transporter / 1,299,288 / 17.53 / 17.14 / 17.56
EG10675 / oppB / oligopeptide ABC transporter / 1,301,017 / 34.00 / 31.95 / 29.65
EG10676 / oppC / oligopeptide ABC transporter / 1,301,995 / 20.69 / 22.93 / 27.21
EG10677 / oppD / oligopeptide ABC transporter / 1,302,879 / 34.35 / 31.93 / 30.18
EG10678 / oppF / oligopeptide ABC transporter / 1,303,906 / 2.11 / 27.81 / 30.46 / 27.17
EG11126 / yciF / conserved protein / 1,313,321 / 0.13 / 0.30 / 0.37 / 0.13
EG10184 / cysB / CysB transcriptional dual regulator / 1,332,076 / 2.02 / 2.18 / 3.06 / 3.13
EG11325 / acnA / aconitase / 1,334,283 / 0.35 / 0.45 / 0.24
EG10809 / pyrF / orotidine-5'-phosphate-decarboxylase / 1,339,947 / 2.29 / 2.26 / 3.31
EG11128 / yciH / putative translation initiation factor / 1,340,683 / 2.23 / 2.45 / 3.18
EG10776 / pspA / negative transcriptional regulator of the psp operon / 1,366,116 / 6.78 / 3.47 / 8.13 / 7.52 / 3.63
EG10777 / pspB / stimulates PspC-mediated transcriptional activation of the psp operon; antitoxin of a PspC-PspB toxin-antitoxin pair / 1,366,864 / 6.80 / 2.91 / 7.81 / 5.61 / 2.35
EG10778 / pspC / PspC transcriptional regulator; toxin of a PspC-PspB toxin-antitoxin pair / 1,367,112 / 6.98 / 2.51 / 6.67 / 5.16 / 2.36
EG10779 / pspD / phage shock protein localized to the peripheral inner membrane / 1,367,417 / 9.51 / 3.25 / 8.81 / 5.02 / 2.60
EG10780 / pspE / thiosulfate sulfurtransferase / 1,367,742 / 5.53 / 2.21 / 3.67 / 2.67
EG10172 / cybB / cytochrome b561 / 1,488,957 / 2.17 / 2.65 / 2.07 / 2.33
EG11219 / ydcA / hypothetical protein / 1,489,710 / 2.30 / 2.73 / 2.79
G6741 / ydcK / putative LpxA-like enzyme / 1,497,592 / 0.38 / 0.38 / 0.32
G6743 / ydcM / putative virulence protein / 1,501,695 / 2.29 / 2.29 / 2.80 / 2.26 / 2.65 / 2.54
G6753 / ydcU / YdcS/YdcT/YdcV/YdcU ABC transporter / 1,512,159 / 0.47 / 0.46 / 0.40 / 0.30
G6755 / ydcW / putative succinate-semialdehyde dehydrogenase / putative aminobutyraldehyde dehydrogenase / 1,513,777 / 0.27 / 0.47 / 0.50 / 0.34
EG10648 / narZ / nitrate reductase Z / 1,536,914 / 0.31 / 0.43 / 0.46 / 0.25
G6786 / xasA / XasA GABA APC transporter / 1,567,254 / 0.19 / 0.32 / 0.09
G6788 / ydeN / putative sulfatase / 1,578,883 / 0.30 / 0.33 / 0.22 / 0.15
G6863 / ydgC / hypothetical protein / 1,679,724 / 2.03 / 2.08 / 2.24
G6866 / uidC / membrane-associated protein / 1,689,692 / 0.50 / 0.48 / 0.20 / 0.31
EG11055 / uidA / beta-glucuronidase / 1,692,380 / 0.43 / 0.26 / 0.42
EG10544 / lpp / murein lipoprotein / 1,755,445 / 2.16 / 2.01 / 2.59 / 3.74 / 2.52 / 2.30
G6906 / csdB / L-selenocysteine lyase (and L-cysteine desulfurase) monomer / 1,757,423 / 0.42 / 0.47 / 0.47
G6907 / sufD / component of SufB-SufC-SufD cysteine desulfurase (SufS) activator complex / 1,758,729 / 0.30 / 0.41 / 0.39 / 0.46
G6908 / sufC / ATPase component of SufB-SufC-SufD cysteine desulfurase (SufS) activator complex / 1,759,816 / 0.35 / 0.40 / 0.43
G6909 / sufB / component of SufB-SufC-SufD cysteine desulfurase (SufS) activator complex / 1,760,596 / 0.30 / 0.46 / 0.40 / 0.40
EG11378 / sufA / scaffold protein for iron-sulfur cluster assembly / 1,762,087 / 0.24 / 0.31 / 0.32 / 0.27
EG10080 / aroH / 2-dehydro-3-deoxyphosphoheptonate aldolase / 1,786,594 / 2.01 / 2.64 / 2.50 / 2.59
EG10881 / rplT / 50S ribosomal subunit protein L20s and regulator / 1,797,525 / 2.13 / 2.71 / 2.55 / 2.33 / 2.23
G6934 / ydjN / part of a kinase / 1,809,069 / 2.38 / 2.63 / 3.05