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Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12.

Sánchez-Romero MA, Busby SJ, Dyer NP, Ott S, Millard AD, Grainger DC - MBio (2010)

Bottom Line: Less SeqA is found in highly transcribed regions, as well as in the ter macrodomain.Using synchronized cultures, we show that SeqA distribution differs with the cell cycle.SeqA remains bound to some targets after replication has ceased, and these targets locate to genes encoding factors involved in nucleotide metabolism, chromosome replication, and methyl transfer.

View Article: PubMed Central - PubMed

Affiliation: School of Biosciences, the University of Birmingham, Edgbaston, Birmingham, United Kingdom.

ABSTRACT
The bacterial SeqA protein binds to hemi-methylated GATC sequences that arise in newly synthesized DNA upon passage of the replication machinery. In Escherichia coli K-12, the single replication origin oriC is a well-characterized target for SeqA, which binds to multiple hemi-methylated GATC sequences immediately after replication has initiated. This sequesters oriC, thereby preventing reinitiation of replication. However, the genome-wide DNA binding properties of SeqA are unknown, and hence, here, we describe a study of the binding of SeqA across the entire Escherichia coli K-12 chromosome, using chromatin immunoprecipitation in combination with DNA microarrays. Our data show that SeqA binding correlates with the frequency and spacing of GATC sequences across the entire genome. Less SeqA is found in highly transcribed regions, as well as in the ter macrodomain. Using synchronized cultures, we show that SeqA distribution differs with the cell cycle. SeqA remains bound to some targets after replication has ceased, and these targets locate to genes encoding factors involved in nucleotide metabolism, chromosome replication, and methyl transfer.

No MeSH data available.


Related in: MedlinePlus

Conservation of GATC motifs in SeqA binding targets. The figure shows a heat map describing the GATC motif contents of 123 bacterial genomes containing a seqA homologue (rows) and a group of genes bound by SeqA in our ChIP-chip analysis (columns). Genes that have a higher frequency of GATC motifs than the genome background are green, and genes with an average or less-than-average GATC motif content are yellow. The genomes are clustered into evolutionary groups. Group 1A contains Enterobacteriaceae, such as E. coli and Shigella, and group 1B also contains Enterobacteriaceae, including Salmonella and Klebsiella. Group 2B contains other gammaproteobacteria, such as Pasteurella multocida. A high-resolution version of this figure, complete with genome accession numbers, is available in the supplemental material (Fig. S3).
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f7: Conservation of GATC motifs in SeqA binding targets. The figure shows a heat map describing the GATC motif contents of 123 bacterial genomes containing a seqA homologue (rows) and a group of genes bound by SeqA in our ChIP-chip analysis (columns). Genes that have a higher frequency of GATC motifs than the genome background are green, and genes with an average or less-than-average GATC motif content are yellow. The genomes are clustered into evolutionary groups. Group 1A contains Enterobacteriaceae, such as E. coli and Shigella, and group 1B also contains Enterobacteriaceae, including Salmonella and Klebsiella. Group 2B contains other gammaproteobacteria, such as Pasteurella multocida. A high-resolution version of this figure, complete with genome accession numbers, is available in the supplemental material (Fig. S3).

Mentions: Since SeqA binding in E. coli K-12 is linked to the local density of GATC motifs, it might be possible to identify putative SeqA binding sites in other bacteria on the basis of their GATC content. Thus, we identified 123 bacterial genomes with a SeqA homologue. We then searched each genome for homologues of the genes listed in Table 1. If a candidate homologue was identified, the sequence was extracted and the density of GATC motifs was calculated for that gene. For each gene, we then compared the GATC density with the average GATC density across the whole of the corresponding genome, and the results are shown in Fig. 7 as a heat map (a higher-resolution version is shown in Fig. S3 in the supplemental material). The figure shows that most of the candidate genes have an increased density of GATC motifs in most genomes. Closer inspection shows that the genomes with SeqA homologues fall into five major evolutionary groups and that the frequency of occurrence of GATC sites in the selected genes is different for each group. The best conservation of above-average GATC frequency is seen in group 1A, which contains E. coli K-12 and closely related organisms. Conversely, there is hardly any retention of higher-than-average GATC frequency in group 2B, containing more distantly related genomes. Note that in many cases, this is because the target gene is simply not present (plotted as zero in Fig. 7). For example, Shewanella frigidimarina lacks mukF, ybiW, and nfrA, while Haemophilus somnus lacks pyrD, smtA, ybiW, etk, potI, potH, nfrA, and ygiQ.


Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12.

Sánchez-Romero MA, Busby SJ, Dyer NP, Ott S, Millard AD, Grainger DC - MBio (2010)

Conservation of GATC motifs in SeqA binding targets. The figure shows a heat map describing the GATC motif contents of 123 bacterial genomes containing a seqA homologue (rows) and a group of genes bound by SeqA in our ChIP-chip analysis (columns). Genes that have a higher frequency of GATC motifs than the genome background are green, and genes with an average or less-than-average GATC motif content are yellow. The genomes are clustered into evolutionary groups. Group 1A contains Enterobacteriaceae, such as E. coli and Shigella, and group 1B also contains Enterobacteriaceae, including Salmonella and Klebsiella. Group 2B contains other gammaproteobacteria, such as Pasteurella multocida. A high-resolution version of this figure, complete with genome accession numbers, is available in the supplemental material (Fig. S3).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2912659&req=5

f7: Conservation of GATC motifs in SeqA binding targets. The figure shows a heat map describing the GATC motif contents of 123 bacterial genomes containing a seqA homologue (rows) and a group of genes bound by SeqA in our ChIP-chip analysis (columns). Genes that have a higher frequency of GATC motifs than the genome background are green, and genes with an average or less-than-average GATC motif content are yellow. The genomes are clustered into evolutionary groups. Group 1A contains Enterobacteriaceae, such as E. coli and Shigella, and group 1B also contains Enterobacteriaceae, including Salmonella and Klebsiella. Group 2B contains other gammaproteobacteria, such as Pasteurella multocida. A high-resolution version of this figure, complete with genome accession numbers, is available in the supplemental material (Fig. S3).
Mentions: Since SeqA binding in E. coli K-12 is linked to the local density of GATC motifs, it might be possible to identify putative SeqA binding sites in other bacteria on the basis of their GATC content. Thus, we identified 123 bacterial genomes with a SeqA homologue. We then searched each genome for homologues of the genes listed in Table 1. If a candidate homologue was identified, the sequence was extracted and the density of GATC motifs was calculated for that gene. For each gene, we then compared the GATC density with the average GATC density across the whole of the corresponding genome, and the results are shown in Fig. 7 as a heat map (a higher-resolution version is shown in Fig. S3 in the supplemental material). The figure shows that most of the candidate genes have an increased density of GATC motifs in most genomes. Closer inspection shows that the genomes with SeqA homologues fall into five major evolutionary groups and that the frequency of occurrence of GATC sites in the selected genes is different for each group. The best conservation of above-average GATC frequency is seen in group 1A, which contains E. coli K-12 and closely related organisms. Conversely, there is hardly any retention of higher-than-average GATC frequency in group 2B, containing more distantly related genomes. Note that in many cases, this is because the target gene is simply not present (plotted as zero in Fig. 7). For example, Shewanella frigidimarina lacks mukF, ybiW, and nfrA, while Haemophilus somnus lacks pyrD, smtA, ybiW, etk, potI, potH, nfrA, and ygiQ.

Bottom Line: Less SeqA is found in highly transcribed regions, as well as in the ter macrodomain.Using synchronized cultures, we show that SeqA distribution differs with the cell cycle.SeqA remains bound to some targets after replication has ceased, and these targets locate to genes encoding factors involved in nucleotide metabolism, chromosome replication, and methyl transfer.

View Article: PubMed Central - PubMed

Affiliation: School of Biosciences, the University of Birmingham, Edgbaston, Birmingham, United Kingdom.

ABSTRACT
The bacterial SeqA protein binds to hemi-methylated GATC sequences that arise in newly synthesized DNA upon passage of the replication machinery. In Escherichia coli K-12, the single replication origin oriC is a well-characterized target for SeqA, which binds to multiple hemi-methylated GATC sequences immediately after replication has initiated. This sequesters oriC, thereby preventing reinitiation of replication. However, the genome-wide DNA binding properties of SeqA are unknown, and hence, here, we describe a study of the binding of SeqA across the entire Escherichia coli K-12 chromosome, using chromatin immunoprecipitation in combination with DNA microarrays. Our data show that SeqA binding correlates with the frequency and spacing of GATC sequences across the entire genome. Less SeqA is found in highly transcribed regions, as well as in the ter macrodomain. Using synchronized cultures, we show that SeqA distribution differs with the cell cycle. SeqA remains bound to some targets after replication has ceased, and these targets locate to genes encoding factors involved in nucleotide metabolism, chromosome replication, and methyl transfer.

No MeSH data available.


Related in: MedlinePlus