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Table 1 Minimal conserved anaerobic transcriptional response shared by D. dadantii 3937 and P. atrosepticum SCRI1043 and its comparison to E. coli.

From: Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria

ASAP Feature ID Gene Name Product Fold change
D. dadantii P. atrosepticum E. coli    D. dadantii P. atrosepticum E. coli
A. Orthologs down-regulated ≥ 3-fold in both D. dadantii and P. atrosepticum
ABF-0016541 ABL-0060576 ABE-0009869 exbB membrane spanning protein in TonB-ExbB-ExbD complex -6.6 -3.5 -3.3
ABF-0020799 ABL-0061445 ABE-0007383 nrdA ribonucleotide reductase of class Ia (aerobic), alpha subunit -4.3 -4.7 -2.2*
ABF-0020798 ABL-0061444 ABE-0007386 nrdB ribonucleotide reductase of class Ia (aerobic), beta subunit -3.7 -3.9 -2.0*
ABF-0017172 ABL-0063446 ABE-0009169 sdaC serine transporter -3.1 -3.2 1.3*
ABF-0020233 ABL-0063426   sfuA iron-binding periplasmic protein -9.1 -26.9  
ABF-0019943 ABL-0062041 ABE-0003583 yceI secreted protein -3.1 -5.0 -6.0
ABF-0019942 ABL-0062042 ABE-0003585 yceJ predicted cytochrome b561 -4.4 -4.3 -8.6
ABF-0020068 ABL-0062100 ABE-0005694 ydiU hypothetical protein -3.4 -4.2 -2.2*
ABF-0015019 ABL-0064500 ABE-0012474 yigI conserved protein -2.9 -7.4 -3.1
ABF-0019535 ABL-0061414 ABE-0001021 ykgM predicted ribosomal protein -97.0 -165.4 -1.4*
ABF-0019536 ABL-0061413 ABE-0285027 ykgO predicted ribosomal protein -66.7 -153.3  
ABF-0017084 ABL-0062748 ABE-0006191 znuA zinc ABC transporter, periplasmic-binding protein ZnuA -4.3 -17.5 -1.2*
ABF-0017082 ABL-0062750 ABE-0006201 znuB high-affinity zinc transport system membrane protein -3.3 -2.9 1.4*
ABF-0017083 ABL-0062749 ABE-0006198 znuC high-affinity zinc transport system ATP-binding protein -3.1 -2.8 -1.1*
ABF-0018178 ABL-0063535    Iron dicitrate-binding protein -10.6 -8.4  
ABF-0018571 ABL-0064593    putative iron ABC transporter permease protein -5.9 -23.3  
ABF-0018572 ABL-0064592    putative iron ABC transporter, periplasmic-binding protein -7.9 -117.8  
ABF-0018573 ABL-0064591    putative iron ABC transporter ATP-binding protein -7.3 -104.7  
ABF-0018864 ABL-0063083    TonB-dependent ferric achromobactin receptor -31.6 -4.9  
ABF-0019222 ABL-0064073    putative ABC transporter substrate-binding protein -16.8 -106.2  
ABF-0019223 ABL-0064074    putative ABC transporter substrate-binding protein -22.8 -47.8  
ABF-0019568 ABL-0061801    putative transport system permease protein -10.1 -32.4  
ABF-0019569 ABL-0061802    putative ABC transporter substrate-binding protein -23.1 -31.3  
ABF-0019570 ABL-0061804    putative ABC transporter substrate-binding protein -16.7 -20.8  
ABF-0019572 ABL-0061805    putative ABC transporter substrate-binding protein -17.0 -13.9  
ABF-0020094 ABL-0060663    ABC-type transporter, periplasmic component -4.5 -6.3  
ABF-0020095 ABL-0060662    ABC transporter, permease protein -5.9 -4.3  
ABF-0020096 ABL-0060661    ABC transporter, permease protein -3.0 -4.4  
ABF-0020097 ABL-0060660    ABC transporter ATP-binding protein -3.4 -3.2  
ABF-0046525 ABL-0064075    ABC transporter substrate-binding protein -81.6 -37.0  
B. Orthologs up-regulated ≥ 3-fold in both D. dadantii and P. atrosepticum
ABF-0020642 ABL-0062590 ABE-0004164 adhE iron-dependent alcohol dehydrogenase 16.8 3.6 3.9
ABF-0018570 ABL-0064258 ABE-0002090 ahpC alkyl hydroperoxide reductase, C22 subunit 2.8 6.1 -2.2*
ABF-0019339 ABL-0060528   budC 2,3-butanediol dehydrogenase 36.8 4.1  
ABF-0018628 ABL-0061786 ABE-0013503 dcuB C4-dicarboxylate transporter DcuB 16.4 66.3 8.5
ABF-0018914 ABL-0063040 ABE-0002776 dps Fe-binding and storage protein 3.2 2.9 -2.5*
ABF-0019603 ABL-0062860 ABE-0003073 focA formate transporter 8.1 4.8 3.1
ABF-0017842 ABL-0064288 ABE-0013604 frdA fumarate reductase (anaerobic) NAD/flavoprotein subunit 7.5 11.2 3.5
ABF-0017841 ABL-0064289 ABE-0013602 frdB fumarate reductase (anaerobic), Fe-S subunit 8.8 8.6 5.3
ABF-0017839 ABL-0064290 ABE-0013598 fr d C fumarate reductase (anaerobic), membrane anchor subunit 7.9 9.6 3.7
ABF-0017837 ABL-0064291 ABE-0013595 frdD fumarate reductase (anaerobic), membrane anchor subunit 7.0 7.8 4.5
ABF-0019825 ABL-0062949 ABE-0002893 grxA glutaredoxin 1,coenzyme for ribonucleotide reductase 4.3 3.1 1.0*
ABF-0017078 ABL-0061498   hoxN high-affinity nickel transport protein 6.7 17.6  
ABF-0017349 ABL-0061473 ABE-0009830 hybB predicted hydrogenase 2 cytochrome b type component 5.4 18.8 2.6*
ABF-0017353 ABL-0061476 ABE-0009824 hybE hydrogenase 2-specific chaperone 5.7 15.3 2.1*
ABF-0017346 ABL-0061471 ABE-0009834 hybO hydrogenase 2, small subunit 3.4 18.1 14.6
ABF-0015747 ABL-0061483 ABE-0008931 hycI protease involved in processing C-terminal end of HycE 9.6 25.8 1.4*
ABF-0015752 ABL-0061495 ABE-0008919 hydN formate dehydrogenase-H, ferredoxin subunit 55.3 183.5 1.7*
ABF-0015735 ABL-0061493 2 orthologs hyfA hydrogenase 4, 4Fe-4S subunit 32.2 128.0 MO
ABF-0015736 ABL-0061492 2 orthologs hyfB hydrogenase 4, membrane subunit 26.7 163.1 MO
ABF-0015737 ABL-0061491 2 orthologs hyfC hydrogenase 4, membrane subunit 10.9 123.6 MO
ABF-0015738 ABL-0061490 ABE-0008185 hyfD hydrogenase 4, membrane subunit 26.2 173.6 -1.7*
ABF-0015739 ABL-0061489 ABE-0008188 hyfE hydrogenase 4, membrane subunit 29.4 72.0 1.5*
ABF-0015740 ABL-0061488 ABE-0008191 hyfF hydrogenase 4, membrane subunit 15.8 57.3 2.7*
ABF-0015741 ABL-0061487 2 orthologs hyfG hydrogenase 4, subunit 26.7 75.1 MO
ABF-0015742 ABL-0061486 ABE-0008942 hyfH hydrogenase 4, Fe-S subunit 17.0 64.9 1.9*
ABF-0015744 ABL-0061485 2 orthologs hyfI hydrogenase 4, Fe-S subunit 17.5 62.2 MO
ABF-0015745 ABL-0061484 2 orthologs hyfJ predicted processing element hydrogenase 4 31.3 46.9 MO
ABF-0017358 ABL-0061480 ABE-0008960 hypB GTP hydrolase involved in nickel liganding into hydrogenases 5.8 41.4 2.3*
ABF-0020729 ABL-0061479 ABE-0008962 hypC [NiFe] hydrogenase metallocenter assembly protein HybG 21.1 18.4 3.8
ABF-0017360 ABL-0061478 ABE-0008965 hypD protein required for maturation of hydrogenases 3.6 31.6 2.4*
ABF-0047122 ABL-0062652 ABE-0006058 manZ mannose-specific enzyme IID component of PTS 3.9 4.1 -2.1*
ABF-0016556 ABL-0060593 ABE-0013865 nrdD anaerobic ribonucleoside-triphosphate reductase 17.8 24.4 4.4
ABF-0016554 ABL-0060592 ABE-0013860 nrdG anaerobic ribonucleotide reductase activating protein 4.9 6.2 4.5
ABF-0017768 ABL-0062712 ABE-0003800 pepT peptidase T 31.3 19.7 3.6
ABF-0019604 ABL-0062861 2 orthologs pflB pyruvate formate lyase I 10.3 3.4 MO
ABF-0174126 ABL-0064936 ABE-0003227 rmf ribosome modulation factor 8.3 3.2 1.9*
ABF-0015967 ABL-0063825 ABE-0008501 trxC thioredoxin 2 7.0 21.3 -3.8
ABF-0016966 ABL-0061596 ABE-0002386 ybfA predicted protein 6.7 3.9 2.2*
ABF-0019390 ABL-0062816 ABE-0003125 ycbJ conserved protein 6.1 4.9 3.3
ABF-0018000 ABL-0062073 ABE-0003740 ycfP conserved protein 3.1 3.2 1.7*
ABF-0020593 ABL-0063322 ABE-0007565 yfbS predicted transporter 3.5 4.6 1.0*
ABF-0020590 ABL-0063324 ABE-0007571 yfbU conserved protein 3.2 7.3 1.4*
ABF-0020347 ABL-0063577 ABE-0008489 yfiD pyruvate formate lyase subunit 18.8 3.1 5.9
ABF-0018102 ABL-0060954 ABE-0010380 yhbU predicted peptidase (collagenase-like) 8.5 25.5 5.9
ABF-0018103 ABL-0060953 ABE-0010382 yhbV predicted protease 9.9 18.0 3.7
ABF-0015647 ABL-0060483 ABE-0010667 yhdH predicted oxidoreductase, Zn-dependent and NAD(P)-binding 4.9 3.0 1.8*
ABF-0020757 ABL-0062521 ABE-0005319 ynfK predicted dethiobiotin synthetase 9.6 16.3 5.3
ABF-0017163 ABL-0063441    putative membrane protein 7.8 8.8  
ABF-0018208 ABL-0060635    hypothetical protein 14.1 30.7  
ABF-0018787 ABL-0063809    lactoylglutathione lyase-like lyase 53.8 3.8  
ABF-0019032 ABL-0061661 ABE-0004921   formate dehydrogenase, cytochrome B556 subunit 24.3 27.1 1.5*
  1. This list of orthologous phytopathogen genes which have a 1-1 relationship according to OrthoMCL are differentially expressed with a 3- fold or more change in gene expression for both orthologs. Where there is a single E. coli ortholog in the group, the fold change is included, and, statistically insignificant values are marked with an asterisk. Several groups have multiple orthologs in E. coli, (indicated by MO) and their expression values are not included. Orthologs showing congruent expression pattern with fold changes > 3 across all three organisms have gene names in bold. The gene names and products were selected from among the three organisms to favor the most correct or most potentially informative and edited slightly to unify the format.
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BMC Genomics

ISSN: 1471-2164

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