TY - JOUR
T1 - Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group A Streptococcus
AU - DebRoy, Sruti
AU - Aliaga-Tobar, Victor
AU - Galvez, Gabriel
AU - Arora, Srishtee
AU - Liang, Xiaowen
AU - Horstmann, Nicola
AU - Maracaja-Coutinho, Vinicius
AU - Latorre, Mauricio
AU - Hook, Magnus
AU - Flores, Anthony R.
AU - Shelburne, Samuel A.
N1 - Funding Information:
This work was supported by RO1 AI089891 (S.A.S) from the National Institutes of Health, CONICYT-PIA Program AFB170001 of the Center for Mathematical Modeling (M.L), FONDECYT N??1190742 (M.L), Center for Genome Regulation FONDAP 15090007 (M.L), Mesa Miner?a?Consorcio de Universidades del Estado de Chile?CUECH (M.L) and Fondo de Innovaci?n para la Competitividad?FIC2018?6ta?regi?n, Gobierno Regional Chile (M.L). We acknowledge the CCSG P30 CA016672 funds for the Bioinformatics Shared Resource and the Sequencing and Microarray facility at MD Anderson Cancer Center. We would like to acknowledge Kunal Rai and Christopher Terranova for their knowledge and guidance in developing ChIP-seq methodology for GAS.
Funding Information:
This work was supported by RO1 AI089891 (S.A.S) from the National Institutes of Health, CONICYT‐PIA Program AFB170001 of the Center for Mathematical Modeling (M.L), FONDECYT N° 1190742 (M.L), Center for Genome Regulation FONDAP 15090007 (M.L), Mesa Minería—Consorcio de Universidades del Estado de Chile—CUECH (M.L) and Fondo de Innovación para la Competitividad—FIC2018—6 región, Gobierno Regional Chile (M.L). We acknowledge the CCSG P30 CA016672 funds for the Bioinformatics Shared Resource and the Sequencing and Microarray facility at MD Anderson Cancer Center. We would like to acknowledge Kunal Rai and Christopher Terranova for their knowledge and guidance in developing ChIP‐seq methodology for GAS. ta
Publisher Copyright:
© 2020 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd.
PY - 2021/6
Y1 - 2021/6
N2 - 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 nonpathogenic 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/ChIP-seq 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 ChIP-seq 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.
AB - 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 nonpathogenic 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/ChIP-seq 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 ChIP-seq 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.
KW - ChIP-seq
KW - HPr-independent CcpA regulation
KW - Streptococcus pyogenes
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U2 - 10.1111/mmi.14667
DO - 10.1111/mmi.14667
M3 - Article
C2 - 33325565
AN - SCOPUS:85098173393
SN - 0950-382X
VL - 115
SP - 1207
EP - 1228
JO - Molecular Microbiology
JF - Molecular Microbiology
IS - 6
ER -