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. 2011 Oct 5;40(3):1009–1020. doi: 10.1093/nar/gkr830

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© The Author(s) 2011. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 3. — Target promoter sequence analysis of DNA damage and repair genes and in vivo DNA-binding activity of Ms6564 assays. (A) Functional categories of Ms6564 target genes in M. smegmatis. The classification and percentage of the target genes were analyzed in the context of COG categories. (B) The IR-containing motif (ACGAGACGGTA CGTCTCGT) was used to search the intergenic regions between M. smegmatis Open Reading Frames (ORFs). The identified promoters of the DNA damage and repair genes containing the motif are blasted and listed. The conserved sequence is highlighted by black backgrounds. The included genes in the same operon were presented in the following brackets. (C) Logo assays for the protected region. The logos were generated by MEME software suite (34). (D) ChIP assays for the association of Ms6564 with DNA damage and repair target genes. ChIP using preimmune (P) or immune sera (I) rose against Ms6564. The DNA samples of the input and ChIP were purified and resuspended in 50 µl TE. DNA recovered from the immunoprecipitates was amplified with primers specific for DNA repair genes or to an unrelated mycobacterial promoter of Ms1432.