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When BvgS is active, BvgA is phosphorylated (BvgA~P), and virulence-activated genes (\n                    <jats:italic>vag<\/jats:italic>\n                    s) are expressed [Bvg(+) mode]. When BvgS is inactive and BvgA is not phosphorylated, virulence-repressed genes (\n                    <jats:italic>vrg<\/jats:italic>\n                    s) are induced [Bvg(\u2212) mode]. Here, we have used transcriptome sequencing (RNA-seq) and reverse transcription-quantitative PCR (RT-qPCR) to define the BvgAS-dependent regulon of\n                    <jats:italic>B.\u00a0pertussis<\/jats:italic>\n                    Tohama I. Our analyses reveal more than 550 BvgA-regulated genes, of which 353 are newly identified. BvgA-activated genes include those encoding two-component systems (such as\n                    <jats:italic>kdpED<\/jats:italic>\n                    ), multiple other transcriptional regulators, and the extracytoplasmic function (ECF) sigma factor\n                    <jats:italic>brpL<\/jats:italic>\n                    , which is needed for type 3 secretion system (T3SS) expression, further establishing the importance of BvgA~P as an apex regulator of transcriptional networks promoting virulence. Using\n                    <jats:italic>in vitro<\/jats:italic>\n                    transcription, we demonstrate that the promoter for\n                    <jats:italic>brpL<\/jats:italic>\n                    is directly activated by BvgA~P. BvgA-FeBABE cleavage reactions identify BvgA~P binding sites centered at positions \u221241.5 and \u221263.5 in\n                    <jats:italic>bprL<\/jats:italic>\n                    . Most importantly, we show for the first time that genes for multiple and varied metabolic pathways are significantly upregulated in the\n                    <jats:italic>B.\u00a0pertussis<\/jats:italic>\n                    Bvg(\u2212) mode. These include genes for fatty acid and lipid metabolism, sugar and amino acid transporters, pyruvate dehydrogenase, phenylacetic acid degradation, and the glycolate\/glyoxylate utilization pathway. Our results suggest that metabolic changes in the Bvg(\u2212) mode may be participating in bacterial survival, transmission, and\/or persistence and identify over 200 new\n                    <jats:italic>vrg<\/jats:italic>\n                    s that can be tested for function.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>IMPORTANCE<\/jats:bold>\n                    Within the past 20\u00a0years, outbreaks of whooping cough, caused by\n                    <jats:italic>Bordetella pertussis<\/jats:italic>\n                    , have led to respiratory disease and infant mortalities, despite good vaccination coverage. This is due, at least in part, to the introduction of a less effective acellular vaccine in the 1990s. It is crucial, then, to understand the molecular basis of\n                    <jats:italic>B.\u00a0pertussis<\/jats:italic>\n                    growth and infection. The two-component system BvgA (response regulator)\/BvgS (histidine kinase) is the master regulator of\n                    <jats:italic>B.\u00a0pertussis<\/jats:italic>\n                    virulence genes. We report here the first RNA-seq analysis of the BvgAS regulon in\n                    <jats:italic>B.\u00a0pertussis<\/jats:italic>\n                    , revealing that more than 550 genes are regulated by BvgAS. We show that genes for multiple and varied metabolic pathways are highly regulated in the Bvg(\u2212) mode (absence of BvgA phosphorylation). Our results suggest that metabolic changes in the Bvg(\u2212) mode may be participating in bacterial survival, transmission, and\/or persistence.\n                  <\/jats:p>","DOI":"10.1128\/mbio.01526-17","type":"journal-article","created":{"date-parts":[[2017,10,10]],"date-time":"2017-10-10T20:10:30Z","timestamp":1507666230000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":72,"title":["The BvgAS Regulon of\n                    <i>Bordetella pertussis<\/i>"],"prefix":"10.1128","volume":"8","author":[{"given":"Kyung","family":"Moon","sequence":"first","affiliation":[{"name":"Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard P.","family":"Bonocora","sequence":"additional","affiliation":[{"name":"Wadsworth Center, New York State Department of Health, Albany, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David D.","family":"Kim","sequence":"additional","affiliation":[{"name":"Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qing","family":"Chen","sequence":"additional","affiliation":[{"name":"Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph T.","family":"Wade","sequence":"additional","affiliation":[{"name":"Wadsworth Center, New York State Department of Health, Albany, New York, USA"},{"name":"Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott","family":"Stibitz","sequence":"additional","affiliation":[{"name":"Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deborah M.","family":"Hinton","sequence":"additional","affiliation":[{"name":"Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiu001"},{"key":"e_1_3_3_3_2","volume-title":"Pertussis (whooping cough): surveillance and reporting","author":"Centers for Disease Control and Prevention","year":"2015","unstructured":"Centers for Disease Control and Prevention . 2015. 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