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. 2008 Aug 27;2(8):e282. doi: 10.1371/journal.pntd.0000282

Table 2. URE3 motif in promoters of genes modulated by a dominant positive URE3-BP.

Pathema Loci ID Annotation Fold Change Position of URE3 5′ of ATG Location of Other URE3 motifs Motif Orientation1
Proteins With Signal Peptides
EHI_062960 membrane protein, receptor-mediated transport2,3 4.19 133 124 TATTCTtTT −
EHI_010850 EhCP-A2 &7 2.38 275 TATTCTATT +
EHI_046650 membrane protein, similar to Gal/GalNAc lectin heavy subunit4 −2.01 134 113 Tt/gTTCTATT −
139
EHI_166370 membrane protein −2.07 182 35 TATTCTATT/g −
EHI_183210 membrane protein4,5 −2.07 209 TtTTCTATT −
EHI_067910 Competence protein ComEC4 −2.16 113 TATTCTtTT +
EHI_084730 multidrug resistance-associated protein2 −2.28 147 TATTCTtTT +
EHI_120930 transmembrane protein kinase4 −2.28 125 140 TATTC/gTATT +
EHI_057430 membrane protein, surface antigen ariel1 family6 −2.47 46 TgTTCTATT −
EHI_145850 membrane protein −2.61 125 TATTGTATT −
EHI_103900 membrane protein, nucleosome-binding protein 1 −3.3 46 127 TA/tTTGTATT −
EHI_132250 membrane protein −3.53 118 TATTGTATT −
EHI_114000 membrane protein −5.26 46 127 TA/tTTGTATT −
EHI_109010 membrane protein6 −5.67 46 TtTTCTATT −
EHI_146100 membrane protein −6.11 46 TtTTCTATT −
EHI_163360 membrane protein6 −6.56 46 TATTGTATT −
Cytoskeletal associated proteins
EHI_154330 Calponin homology domain2 −3.38 261 343 TATTCTtTT −
Metabolic enzymes
EHI_065250 membrane protein, Lecithin:cholesterol acyltransferase 5.25 106 TATTCTtTT −
EHI_079300 acyl-CoA synthetase 2.98 362 TATTCTATT +
EHI_092490 Protein with a weak similarity to sulfotransferases2,7 2.58 78 217 TATTC/gTT/tTT +
EHI_090430 Protein with a weak similarity to sulfotransferase7,8 2.52 223 TtTTCTATT −
EHI_005060 Fe-hydrogenase9 2.35 140 TtTTCTATT −
EHI_185240 long-chain-fatty-acid--CoA ligase −2.43 157 193 TtTTCTATT −
DNA transcription/translation
EHI_004480 basic leucine zipper protein3 2.36 80 89 TA/tTTCTATT −
EHI_059690 chromosome segregation COG 1196 −2.33 51 TATTCTtTT −
EHI_158020 transcription initiation factor IIIB chain BRF −2.57 35 TATTCTtTT −
EHI_000780 chromodomain-helicase-DNA-binding protein4 −2.94 128 TATTCTtTT −

Identity (Pathema Locus number) and gene annotation of significantly modulated genes are shown in conjunction with the observed change between induced EF(2)mutURE3-BP and STOP- EF(2)mutURE3-BP strains. The distance between the URE3 motif and the presumed initiating ATG codon is shown as is the position of other potential URE3 motifs, the promoter consensus URE3 motif, and orientation.

1

If the motif is present in the promoter in a 5′ to 3′ direction this is indicated by (+) and on the reverse strand by (−).

2

These transcripts were decreased in recent clinical isolates [4]

3

Was modestly induced by tetracyclin at below threshold values

4

These transcripts were increased in recent clinical isolates [4]

5

This probe set recognizes a gene shown to be up regulated in HM-1:IMSS compared to a Rahman strain [3]

6

A signal peptide was found in either the 5′ extended open reading frame or 3′ of initiating ATG, the position of URE3 motif is shown from the newly designated initiating ATG

7

Annotation on the basis of homology to known sulfotransferases

8

This transcript was also significantly increased in the EF(2)mutURE3-BPuninduced ameba compared to the uninduced control.

9

This gene was described by Nixon et al and has been shown to be up regulated in HM-1:IMSS compared to a Rahman strain [3],[45]