Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group A Streptococcus.

DebRoy, S.; Tobar, V. A.; Galvez, G.; Arora, S.; Liang, X.; Horstmann, N. M.; Maracaja-Coutinho, V.; Latorre, M.; Hook, M.; Flores, A. R.; Shelburne, S.

doi:10.1101/2020.08.28.272682

bioRxiv · 10.1101/2020.08.28.272682

Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group A Streptococcus.

DebRoy, S.·Tobar, V. A.·Galvez, G.·Arora, S.·Liang, X.·Horstmann, N. M.·Maracaja-Coutinho, V.·Latorre, M.·Hook, M.·Flores, A. R.·Shelburne, S.

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Abstract

Catabolite control protein A (CcpA) is a master regulator of carbon source utilization and contributes to the virulence of numerous medically important Gram-positive bacteria. Most functional assessments of CcpA, including interaction with its key co-factor HPr, have been performed in non-pathogenic bacteria. In this study we aimed to identify the in vivo DNA binding profile of CcpA and assess the extent to which HPr is required for CcpA-mediated regulation and DNA binding in the major human pathogen group A Streptococcus (GAS). Using a combination RNAseq/ChIPseq approach, we found that CcpA affects transcript levels of 514 of 1667 GAS genes (31%) whereas direct DNA binding was identified for 105 GAS genes. Three of the directly regulated genes encode the key GAS virulence factors Streptolysin S, PrtS (IL-8 degrading proteinase), and SpeB (cysteine protease). Mutating CcpA Val301 to Ala (strain 2221-CcpA-V301A) abolished interaction between CcpA and HPr and impacted the transcript levels of 205 genes (40%) in the total CcpA regulon. By ChIPseq analysis, CcpAV301A bound to DNA from 74% of genes bound by wild-type CcpA, but generally with lower affinity. These data delineate the direct CcpA regulon and clarify the HPr-dependent and independent activities of CcpA in a key pathogenic bacterium. Data sharing and data availabilityThe data that support the findings of this study are available from the corresponding author upon reasonable request.

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DebRoy, S., Tobar, V. A., Galvez, G., Arora, S., Liang, X., Horstmann, N. M., Maracaja-Coutinho, V., Latorre, M., Hook, M., Flores, A. R., Shelburne, S.. 2020-08-28. Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group A Streptococcus.. https://doi.org/10.1101/2020.08.28.272682

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