Table 1

Mutations that occurred in the evolved PB12 strain during the adaptive process
A) Gene Basic description Mutations
Hypothetical genes JM101 and PB11 PB12 Nucleotide Pos/Change
gfcD* Hypothetical lipoprotein. GTA cTA 916 306 V-L
yafV* Predicted C-N hydrolase family amidase, NAD(P)-binding. CGC CaC 452 151 R-H
+ytfR(WG) Putative ATP-binding component of a galactose ABC transporter. GTC GcC 602 201 V-A
Metabolism and Transport JM101 and PB11 PB12 Nucleotide Pos/Change
+actP* Acetate/glycolate permease in the solute:sodium symporter (SSS) family. GTA GcA 731 244 V-A
arnT* L-Ara4N transferase catalyzes addition of L-Ara4N to lipid A under some conditions. TAC TgC 1193 398 Y-C
+chbC* Integral membrane transport protein, member of the chitobiose PTS transporter. GCG GtG 347 116 A-V
+csgF(WG) Curli secretion and assembly complex. AAU AgU 89 30 N-S
+dgoT* Probable galactonate transporter, member of the major facilitator superfamily (MFS) of transporters. GAT GgT 653 218 D-G
dhaM* Dihydroxyacetone kinase subunit M, homologous to certain PTS components. TGG TGa 1038 346 W-stop
+dppF* ATP-binding component of the dipeptide ABC transporter. CAC CgC 680 227 H-R
fdhD* Protein with unknown function, required for wild-type formate dehydrogenase-N activity. AGT gGT 652 218 S-G
fimH* Minor fimbrial subunit, D-mannose specific adhesin, subunit of fimbrial complex. ACT gCT 535 179 T-A
glpT* Major uptake transporter for glycerol-3-phosphate, belongs to the major facilitator superfamily (MFS). CCG CtG 416 139 P-L
rfe* Undecaprenyl-phosphate α-N-acetylglucosaminyl transferase . GCC aCC 238 80 A-T
+sucA* E1(0) component of the oxoglutarate dehydrogenase complex. GAT GAa 372 124 D-E
ydiQ* Putative subunit of YdiQ-YdiR flavoprotein. GTG GcG 218 73 V-A
Regulatory and putative regulatory genes JM101 and PB11 PB12 Nucleotide Pos/Change
+arcB* Hybrid protein sensory kinase, member of two-component system. TAC TgC 212 71 Y-C
+barA* Hybrid protein sensory kinase, member of two-component system. TTC cTC 1096 366 F-L
+rna* RNase I, cleaves phosphodiester bond between any two nucleotides. GCC aCC 268 90 A-T
+rpoD* Sigma 70 factor, subunit of RNA polymerase. GTT aTT 1744 582 V-I
+rssA* Hypothetical protein, coded by a gene that is part of therssABoperon. CGC CaC 773 258 R-H
+yjjU* Conserved hypothetical protein, could work as a transcriptional protein. ACT gCT 338 179 T-A
+ypdA* Predicted sensory kinase member of two-component system. GCG tCC 598 200 A-S
B) Gene Basic description Mutations
ptsP Member of a second PTS chain involved in nitrogen metabolism Present Absent --- ---
rppH RNA pyrophosphohydrolase that initiates mRNA degradation by hydrolysis of the 5'-triphosphate end. Present Absent --- ---
ygdT Hypothetical protein. Present Absent --- ---
mutH dGATC endonuclease in the MutHLS complex, the methyl-directed mismatch repair pathway. Present Absent --- ---
ygdQ Putative transport protein. Present Absent --- ---
ygdR Predicted protein. Present Absent --- ---
tas Putative NAD(P)-linked reductase that acts in starvation-associated mutations. Present Absent --- ---
lplT Lysophospholipid transporter (LplT). Present Absent --- ---
aas 2-acylglycerophosphoethanolamine acyltransferase/acyl-ACP synthetase. Present Absent --- ---
omrA Small RNA that is involved in regulating the protein composition of the outer membrane. Present Absent --- ---
omrB Small RNA that is involved in regulating the protein composition of the outer membrane. Present Absent --- ---
galR DNA-binding transcription factor; represses transcription of the operons involved in transport and catabolism of D-galactose. Present Absent --- ---

Table 1A presents the 23 non synonymous point mutations in structural genes that changed the code for a different amino acid when compared to the parental PB11 and JM101 strains genomes. The asterisks in the table indicate the 21 non-synonymous point mutations detected by both Roche NimbleGen Inc. (RN) and Winter Genomics Inc. (WG) methods. In addition 22 synonymous point mutations in different genes were also detected (Tables S1 and S2 in Additional file 1 and Additional file 2). The regulatory and possible regulatory genes analyzed in this study are in bold letters. The mutations in these seven regulatory and possible regulatory genes and in seven additional genes were confirmed by the Sanger methodology and are labeled with a +. 26 (21+5) point mutations in 26 genes were detected by RN, 5 of them were false positive. 27 (21+6) point mutations in 27 genes were detected by WG. In addition to the 21 mutations shared with RN, only two of these point mutations (noted as WG) were confirmed by the Sanger methodology. Additional file 1 and Additional file 2 (Tables S1 and S2) include the data from RN and WG. Table 1B presents the absent genes in the largest deletion reported by both companies. (Figures. 2, 3, 4 and S1, presented in Additional file 3). Basic descriptions of these genes were taken from www.ecocyc.org.

Aguilar et al.

Aguilar et al. BMC Genomics 2012 13:385   doi:10.1186/1471-2164-13-385

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