Table S5 --- Version 1: Strongest occurrences of a putative C. crescentus xylose-induction motif
upstream of X. campestris and X. citri genes
Genes Diverging from
Intergenic Regiona
XCC1727
XCC4100b
XCC4102b, c
XCC4119/XCC4120
XAC1267
XAC2998
XAC4193/XAC4194
XAC4225b, d
XAC4255/XAC4256
Motif Sequence
AGCTTAGGTAGCGCTATCTC
CGCAATGTTAGCGCTACCAA
ATAAATGGTAGCGCAACCAT
CCGGATGTTAGCGCTACCAA
CGGATTGGTAGCGCTACCGA
CGGCATGTTAGCGCTATCAC
CTTGATGTTAGCGCTAACAC
GAAAATGTTAGCGCTACCAC
CGGGATGTTAGCGCTAACAA
Bases from
start codon
161
123
-144
164/199
197
424
413/265
133
163/195
a
X. campestris genes start with XCC and X. citri genes start with XAC.
b
Two promoters diverge from the intergenic region. Only the one with a putative transcription unit
containing a xylose-related gene is included.
c
The motif was originally identified in the region upstream XCC4101. Inspection of nearby genes
suggested that it might actually control the putative transcription unit starting with XCC4102 which codes
for among other things a xylosidase/arabinosidase (XCC4105).
d
Only the highest scoring motif in the region is shown.
Table S5 --- Version 2: Strongest occurrences of a putative C. crescentus xylose-induction motif
upstream of X. campestris and X. citri genes. Genes predicted to be in transcription units with genes
downstream of the motif are shown indented. Annotations and gene names were taken from GenBank (1).
Putative Transcription Units Diverging from
Intergenic Region with Motif a
XCC1727 chemotaxis protein, mcpA
XCC4100 xylose isomerase, xylA b
XCC4102 alpha-glucuronidase, aguA b, c
XCC4103 sialic acid-specific 9-O-acetylesterase
XCC4104 starvation sensing protein, rspA
XCC4105 xylosidase/arabinosidase, xylB
XCC4106 glucan 1,4-beta-glucosidase
XCC4119 putative hexuronate transporter, exuT
XCC4118 xylanase, xynB
XCC4117 hexuronic acid isomerase, hrmI/
XCC4120 TonB-dependent receptor d
XCC4121 transport protein, xylP
XCC4122 xylosidase/arabinosidase, xsa
XAC1267 Hsp90xo protein
XAC1268 conserved hypothetical protein
XAC2998 TonB-dependent receptor
XAC4193 two-component system sensor protein /
XAC4194 conserved hypothetical protein
XAC4225 xylose isomerase, xylA b
XAC4255 hexuranate transporter, exuT
XAC4254 xylanase, xynB
XAC4253 conserved hypothetical protein
XAC4252 xylanase, xynB
XAC4251 hexuronic acid isomerase, hrmI/
XAC4256 TonB-dependent receptor d
XAC4257 transport protein, xylP
XAC4258 xylosidase, xsa
Motif Sequence
AGCTTAGGTAGCGCTATCTC
CGCAATGTTAGCGCTACCAA
ATAAATGGTAGCGCAACCAT
Bases from
Start Codon
of First
Gene
161
123
-144
CCGGATGTTAGCGCTACCAA
164/199
CGGATTGGTAGCGCTACCGA
197
CGGCATGTTAGCGCTATCAC
CTTGATGTTAGCGCTAACAC
424
413/265
GAAAATGTTAGCGCTACCAC
CGGGATGTTAGCGCTAACAA
133
163/195
a
X. campestris genes start with XCC and X. citri genes start with XAC.
b
Two promoters diverge from the intergenic region. Only the one with a putative transcription unit
containing a xylose-related gene is included.
c
The motif was originally identified in the region upstream XCC4101. Inspection of nearby genes
suggested that it might actually control the putative transcription unit starting with XCC4102 which codes
for among other things a xylosidase/arabinosidase (XCC4105).
d
The intergenic space between XCC4120 and XCC4121 and between XAC4256 and XAC4257 is greater
than the 70 bases used as the cutoff for predicting transcription piece in the rest of the table. The additional
genes are included because of their involvement with xylose catabolism.
References
1.
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