Role of SeqA and Dam in Escherichia coli gene expression: a global/microarray analysis - PubMed (original) (raw)

Role of SeqA and Dam in Escherichia coli gene expression: a global/microarray analysis

Anders Løbner-Olesen et al. Proc Natl Acad Sci U S A. 2003.

Abstract

High-density oligonucleotide arrays were used to monitor global transcription patterns in Escherichia coli with various levels of Dam and SeqA proteins. Cells lacking Dam methyltransferase showed a modest increase in transcription of the genes belonging to the SOS regulon. Bacteria devoid of the SeqA protein, which preferentially binds hemimethylated DNA, were found to have a transcriptional profile almost identical to WT bacteria overexpressing Dam methyltransferase. The latter two strains differed from WT in two ways. First, the origin proximal genes were transcribed with increased frequency due to increased gene dosage. Second, chromosomal domains of high transcriptional activity alternate with regions of low activity, and our results indicate that the activity in each domain is modulated in the same way by SeqA deficiency or Dam overproduction. We suggest that the methylation status of the cell is an important factor in forming and/or maintaining chromosome structure.

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Figures

Figure 1

Figure 1

Gene expression of the gat operon and the flu gene. (A) Gene expression data from the gat operon region are comparisons between MG1655 seqA (yellow), MG1655 dam-13_∷Tn_9 (red), or MG1655 carrying plasmid pTP166 (Dam overproducer, black) and WT MG1655. The genes are listed in order of location on the chromosome, from b2086 to yegX. (B) Gene expression data for the flu and neighboring genes in MG1655 containing plasmid pTP166 compared with WT. Gene expression data were corrected for gene dosage as described in the legend to Table 3.

Figure 2

Figure 2

Expression of individual genes as a function of position on the chromosome. All genes for which a “present” call was obtained were plotted relative to WT as a function of position along the chromosome. The chromosome is linearized at a position directly opposite oriC. The replication origin has position 0 on the abscissa. (A) MG1655 seqA. (B) MG1655/pTP166 (Dam overproducer). (C) MG1655 dam-13_∷Tn_9. Trendlines for the gene expression data are presented in A and B. All points above the trendline in A, i.e., genes that were derepressed in the seqA mutant are plotted as green dots, and all genes that were repressed in the seqA mutant as red dots. Expression data from individual genes in B and C have the same color assignment as in A (red and green dots).

Figure 3

Figure 3

Chromosomal domains. A moving window representing the average expression of 50 expressed genes (data from Fig. 2) is plotted as a function of gene position on the chromosome and relative to WT. The chromosome is linearized at a position directly opposite oriC. The replication origin has position 0 on the abscissa. (A) MG1655 seqA. (B) MG1655/pTP166 (Dam overproducer). (C) MG1655 dam-13_∷Tn_9. The flu gene and the plasmid-encoded dam gene were omitted from the analysis of the Dam overproducing strain presented in B.

Figure 4

Figure 4

Expression domains in the vicinity of oriC. A moving window representing the average expression of 50 expressed genes is plotted as a function of gene position on the chromosome and relative to WT. Blue, MG1655 seqA; orange, MG1655/pTP166 (Dam overproducer), red-violet, MG1655 dam-13_∷Tn_9; green, MG1655/pFHC539 (DnaA overproducer). Blue, orange, and red-violet curves are replotted from Fig. 3.

Figure 5

Figure 5

Peaks and troughs observed in the comparison of MG1655 seqA with WT are inversely correlated with the transcriptional intensity in regions of the MG1655 (WT) chromosome. The red curve represents the seqA/WT comparison from Fig. 3_A_. The blue curve is a moving window of the primary gene expression values of 50 genes (scanning units) on the MG1655 chromosome.

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