Table S2: Transcriptional Units (Tus) Differentially Regulated by E. Coli Sxy Expression

Table S2: Transcriptional Units (TUs) differentially regulated by E. coli sxy expression.

TU numbers correspond to those in Fig. 4. Functional categories: C: Energy production and conversion, E: Amino acid transport and metabolism, F: Nucleotide transport and metabolism, H: Coenzyme transport and metabolism, G: Carbohydrate transport and metabolism, J: Translation, ribosomal structure and biogenesis, K: transcription, L: Replication, recombination and repair, M: Cell wall/membrane/envelope biogenesis, N: Cell motility, O: Posttranslational modification, protein turnover, chaperones, R: General function prediction only, S: function unknown, T: Signal transduction mechanisms, U: Intracellular trafficking, secretion, and vesicular transport. *: replaces b1437.

competence gene homologues:

TUGene namePredicted FunctionCOGFunctional Category

16b0913ycaIconserved inner membrane protein, rec-2 homologueCOG0658R

18b0106hofCfimbriae biogenesisCOG1459NU

18b0107hofBfimbriae biogenesisCOG2804NU

18b0108ppdDpilus subunit (pilin)COG2165NU

20b3391hofQpredicted fimbrial transporterCOG1450NU

20b3392hofPpredicted inner membrane hypothetical proteinnot availablen/a

20b3393hofOpredicted inner membrane hypothetical proteinnot availablen/a

20b3394hofNpredicted inner membrane fimbrial assembly proteinCOG3166NU

20b3395hofMpredicted periplasmic pilus assembly proteinCOG1555L

21b2950yggRputative ATP-binding protein, pilus retraction ATPaseCOG2805NU

28b3765yifBpredicted ATP-dependent protease, comM homologueCOG0606O

30b2823ppdCprepilin peptidase dependent protein CCOG2165NU

30b2824ygdBhypothetical proteinnot availablen/a

30b2825ppdBprepilin peptidase dependent protein BCOG4795U

30b2826ppdAprepilin peptidase dependent protein ACOG2165NU

33b0442ybaVcompetence protein ComEA homolog, function unknownCOG1555L

replication, recombination and repair:

TUGene namePredicted FunctionCOGFunctional Category

1b3645dinDDNA damage inducible proteinCOG0214L

4b0799dinGprobably ATP-dependent helicaseCOG1199KL

8b4059ssbcytoplasmic ssDNA-binding proteinCOG0629L

11b2733mutSmethyl-directed mismatch repairCOG0249L

15b0228yafMputative transposaseCOG1943L

27b2798xniExoIX, 5'-3' exonucleaseCOG0258L

32b3647ligBputative enzyme involved in DNA metabolic processCOG0272L

68b3863polADNA polymerase ICOG0749L

72b4326yjiDDNA replication/recombination/repair proteinnot availablen/a

79b2819recDATP-dependent dsDNA/ssDNA exonuclease V subunitCOG0507L

79b2820recBATP-dependent dsDNA/ssDNA exonuclease V subunitCOG1074L

b3638yicRDNA repair protein RadCCOG2003L

transcription:

TUGene namePredicted FunctionCOGFunctional Category

2b3934cytRtranscriptional regulatorCOG1609K

6b2898ygfZtRNA-modifying protein; folate-dependentCOG0354R

7b2897ygfYtranscriptional regulationCOG2938S

24b1438ydcQpredicted DNA-binding transcriptional regulator COG1598S

26b3890yiiFconserved protein, unknown functionnot availablen/a

69b0294matAputative transcriptional regulator, lux regulonCOG2771K

77b4327yjiEputative transcriptional regulator LYSR-typeCOG0583K

80b1439ydcRpredicted transcriptional regulator / aminotransferaseCOG1167KE

transposases:

TUGene namePredicted FunctionCOGFunctional Category

3b3411yhgApredicted transposaseCOG5464S

13b2305yfcIpredicted transposaseCOG5464S

29b4338yjiPpredicted transposase, PSEUDOGENEnot availablen/a

29b4339yjiPpredicted transposase, PSEUDOGENEnot availablen/a

34b2244yfaDpredicted transposaseCOG5464S

hypothetical proteins:

TUGene namePredicted FunctionCOGFunctional Category

7b2896ygfXhypothetical proteinnot availablen/a

17b1289ycjDhypothetical proteinCOG2852S

23b4532*yncNYcfA-like proteinnot availablen/a

31b2272yfbMhypothetical proteinnot availablen/a

74b0235ykfJconserved protein, PSEUDOGENECOG1690S

76b3554yiaFhypothetical proteinnot availablen/a

toxin-antitoxin:

TUGene namePredicted FunctionCOGFunctional Category

9b3129sohApredicted antitoxin of the SohA-YhaV toxin-antitoxin systemCOG2002K

9b3130yhaVpredicted toxin of the SohA-YhaV toxin-antitoxin systemnot availablen/a

12b1420mokBregulatory peptide whose translation enables hokB expressionnot availablen/a

19b0018mokCregulatory peptide whose translation enables hokC expressionnot availablen/a

24b3082ygjMpredicted DNA-binding transcriptional regulatorCOG5499K

24b3083ygjNhypothetical proteinCOG4680S

25b4224chpSantitoxin of the ChpB-ChpS toxin-antitoxin systemCOG2336T

25b4225chpBtoxin of the ChpB-ChpS toxin-antitoxin systemCOG2337T

71b0245ykfItoxin of the YkfI-YafW toxin-antitoxin systemnot availablen/a

73b1562hokDpolypeptide destructive to membrane potential hokDnot availablen/a

metabolism:

TUGene namePredicted FunctionCOGFunctional Category

10b3648gmkguanylate kinase, GMP recyclingCOG0194E

14b2936yggGUncharacterized metalloproteaseCOG0501O

75b0325yahKZn-dependent alcohol dehydrogenaseCOG1064C

78b0032carAglutamine amidotransferaseCOG0505EF

79b2821ptrAperiplasmic proteaseCOG1025O

81b0443ybaWPutative acyl-CoA thioester hydrolaseCOG0824R

translation:

TUGene namePredicted FunctionCOGFunctional Category

5b2569lepAGTP-binding elongation factorCOG0481M

other:

TUGene namePredicted FunctionCOGFunctional Category

70b3334gspMgeneral secretion pathway protein Mnot availablen/a

22b2700ygaDCinA-family proteinCOG1546R

82b1015putPmajor sodium/proline symporterCOG0591ER

83b2752cysDATP:sulfurylase, subunit 2COG0175EH

84b2778ygcGhypothetical proteinCOG1512R

85b4109yjdAputative vimentinCOG0699R

86b3988rpoCRNA Polymerase subunitCOG0086K

σ32 regulon:

TUGene namePredicted FunctionCOGFunctional Category

35b3931hslUheat shock proteinCOG1220O

36b3498prlCtrypsin-like proteinaseCOG0339E

37b0439lonDNA-binding, ATP-dependent proteaseCOG0466O

38b0473htpGchaperone Hsp90, heat shock proteinCOG0326O

39b0492ybbNputative thioredoxin-like proteinCOG3118O

40b1060bssSbiofilm regulatornot availablen/a

41b1322ycjFputative membrane proteinCOG3768S

42b2592clpBheat shock protein, proteaseCOG0542O

43b2614grpEheat shock protein, proteaseCOG0576O

44b0014dnaKchaperoneCOG0443O

45b2699recADNA-dependent ATPaseCOG0468L

46b0966hspQheat shock proteinCOG3785S

47b3686ibpB16 kDa heat shock proteinCOG0071O

47b3687ibpAheat shock proteinCOG0071O

48b3635mutMDNA repair proteinCOG0266L

49b4140fxsAinner membrane protein of unknown functionCOG3030R

50b0631ybeDhypothetical proteinCOG2921S

FlhDC / FliA regulon:

TUGene namePredicted FunctionCOGFunctional Category

51b3417malPcarbohydrate / polysaccharide catabolisisCOG0058G

52b4355tsrinner membrane taxisCOG0840NT

53b3072aeraerotaxis sensor receptor, flavoproteinCOG0840NT

54b1881cheZCheY protein phophatase, chemotactic responseCOG3143NT

54b1885tapmethyl-accepting chemotaxis protein IVCOG0840NT

55b1924fliDflagellar biosynthesis, filament capping proteinCOG1345N

55b1925fliSflagellar biosynthesis, repressor of class 3a and 3b operonsCOG1516NO

55b1926fliTflagellar biosynthesis; repressor of class 3a and 3b operonsnot availablen/a

56b1421trginner membrane taxisCOG0840NT

57b1887cheWpositive regulator of CheA protein activityCOG0835NT

57b1888cheAsensory transducer kinaseCOG0643NT

57b1889motBenables flagellar motor rotationCOG1360N

58b1070flgNflagellar chaperoneCOG3418NO

58b1071flgManti-sigma factor of FliACOG2747KN

58b1072flgAflagellar biosynthesis, assembly of basal-body periplasmic P ring COG1261N

59b1944fliLflagellar biosynthesisCOG1580N

59b1945fliMflagellar biosynthesis, component of motor switch and energizingCOG1868N

59b1948fliPflagellar biosynthesisCOG1338NU

59b1950fliRflagellar biosynthesisCOG1684NU

60b1566flxAQin prophage; FliA flagella regulonCOG0093J

61b1923fliCflagellar biosynthesis, flagellinCOG1344N

62b1938fliFflagellar biosynthesis, basal-bodyCOG1766NU

62b1939fliGflagellar biosynthesis, component of motor switch and energizingCOG1536N

62b1940fliHflagellar biosynthesis, export of flagellar proteinsCOG1317NU

63b1921fliZflagella regulatornot availablen/a

63b1922fliAalternative sigma factor, regulator of flagellar operonsCOG1191NT

64b3525yhjHEAL domain protein involved in flagellar functionCOG2200T

65b4035malKATP-binding component of transport system for maltoseCOG3839G

65b4036lamBmaltose high-affinity receptorCOG4580G

66b1073flgBflagellar biosynthesis cell-proximal portion of basal-body rodCOG1815N

66b1074flgCflagellar biosynthesis, cell-proximal portion of basal-body rodCOG1558N

66b1075flgDflagellar biosynthesis, initiation of hook assemblyCOG1843N

66b1076flgEflagellar biosynthesis, hook proteinCOG1749N

66b1077flgFflagellar biosynthesis, cell-proximal portion of basal-body rodCOG4787N

66b1078flgGflagellar biosynthesis, cell-distal portion of basal-body rodCOG4786N

67b4034malEperiplasmic maltose-binding proteinCOG2182G