Nitrogen and Carbon Status Are Integrated at the Transcriptional Level by the Nitrogen Regulator NtrC <italic toggle="yes">In Vivo</italic>

ABSTRACT Nitrogen regulation in Escherichia coli is a model system for gene regulation in bacteria. Growth on glutamine as a sole nitrogen source is assumed to be nitrogen limiting, inferred from slow growth and strong NtrB/NtrC-dependent gene activation. However, we show that under these conditions...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Jörg Schumacher, Volker Behrends, Zhensheng Pan, Dan R. Brown, Franziska Heydenreich, Matthew R. Lewis, Mark H. Bennett, Banafsheh Razzaghi, Michal Komorowski, Mauricio Barahona, Michael P. H. Stumpf, Sivaramesh Wigneshweraraj, Jacob G. Bundy, Martin Buck
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2013
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/c6ca6230e20b4eb9b6fba345e8f705e3
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:c6ca6230e20b4eb9b6fba345e8f705e3
record_format	dspace
spelling	oai:doaj.org-article:c6ca6230e20b4eb9b6fba345e8f705e32021-11-15T15:42:32ZNitrogen and Carbon Status Are Integrated at the Transcriptional Level by the Nitrogen Regulator NtrC <italic toggle="yes">In Vivo</italic>10.1128/mBio.00881-132150-7511https://doaj.org/article/c6ca6230e20b4eb9b6fba345e8f705e32013-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00881-13https://doaj.org/toc/2150-7511ABSTRACT Nitrogen regulation in Escherichia coli is a model system for gene regulation in bacteria. Growth on glutamine as a sole nitrogen source is assumed to be nitrogen limiting, inferred from slow growth and strong NtrB/NtrC-dependent gene activation. However, we show that under these conditions, the intracellular glutamine concentration is not limiting but 5.6-fold higher than in ammonium-replete conditions; in addition, α-ketoglutarate concentrations are elevated. We address this glutamine paradox from a systems perspective. We show that the dominant role of NtrC is to regulate glnA transcription and its own expression, indicating that the glutamine paradox is not due to NtrC-independent gene regulation. The absolute intracellular NtrC and GS concentrations reveal molecular control parameters, where NtrC-specific activities were highest in nitrogen-starved cells, while under glutamine growth, NtrC showed intermediate specific activity. We propose an in vivo model in which α-ketoglutarate can derepress nitrogen regulation despite nitrogen sufficiency. IMPORTANCE Nitrogen is the most important nutrient for cell growth after carbon, and its metabolism is coordinated at the metabolic, transcriptional, and protein levels. We show that growth on glutamine as a sole nitrogen source, commonly assumed to be nitrogen limiting and used as such as a model system for nitrogen limitation, is in fact nitrogen replete. Our integrative quantitative analysis of key molecules involved in nitrogen assimilation and regulation reveal that glutamine is not necessarily the dominant molecule signaling nitrogen sufficiency and that α-ketoglutarate may play a more important role in signaling nitrogen status. NtrB/NtrC integrates α-ketoglutarate and glutamine signaling—sensed by the UTase (glnD) and PII (glnB), respectively—and regulates the nitrogen response through self-regulated expression and phosphorylation-dependent activation of the nitrogen (ntr) regulon. Our findings support α-ketoglutarate acting as a global regulatory metabolite.Jörg SchumacherVolker BehrendsZhensheng PanDan R. BrownFranziska HeydenreichMatthew R. LewisMark H. BennettBanafsheh RazzaghiMichal KomorowskiMauricio BarahonaMichael P. H. StumpfSivaramesh WigneshwerarajJacob G. BundyMartin BuckAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 4, Iss 6 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Jörg Schumacher Volker Behrends Zhensheng Pan Dan R. Brown Franziska Heydenreich Matthew R. Lewis Mark H. Bennett Banafsheh Razzaghi Michal Komorowski Mauricio Barahona Michael P. H. Stumpf Sivaramesh Wigneshweraraj Jacob G. Bundy Martin Buck Nitrogen and Carbon Status Are Integrated at the Transcriptional Level by the Nitrogen Regulator NtrC <italic toggle="yes">In Vivo</italic>
description	ABSTRACT Nitrogen regulation in Escherichia coli is a model system for gene regulation in bacteria. Growth on glutamine as a sole nitrogen source is assumed to be nitrogen limiting, inferred from slow growth and strong NtrB/NtrC-dependent gene activation. However, we show that under these conditions, the intracellular glutamine concentration is not limiting but 5.6-fold higher than in ammonium-replete conditions; in addition, α-ketoglutarate concentrations are elevated. We address this glutamine paradox from a systems perspective. We show that the dominant role of NtrC is to regulate glnA transcription and its own expression, indicating that the glutamine paradox is not due to NtrC-independent gene regulation. The absolute intracellular NtrC and GS concentrations reveal molecular control parameters, where NtrC-specific activities were highest in nitrogen-starved cells, while under glutamine growth, NtrC showed intermediate specific activity. We propose an in vivo model in which α-ketoglutarate can derepress nitrogen regulation despite nitrogen sufficiency. IMPORTANCE Nitrogen is the most important nutrient for cell growth after carbon, and its metabolism is coordinated at the metabolic, transcriptional, and protein levels. We show that growth on glutamine as a sole nitrogen source, commonly assumed to be nitrogen limiting and used as such as a model system for nitrogen limitation, is in fact nitrogen replete. Our integrative quantitative analysis of key molecules involved in nitrogen assimilation and regulation reveal that glutamine is not necessarily the dominant molecule signaling nitrogen sufficiency and that α-ketoglutarate may play a more important role in signaling nitrogen status. NtrB/NtrC integrates α-ketoglutarate and glutamine signaling—sensed by the UTase (glnD) and PII (glnB), respectively—and regulates the nitrogen response through self-regulated expression and phosphorylation-dependent activation of the nitrogen (ntr) regulon. Our findings support α-ketoglutarate acting as a global regulatory metabolite.
format	article
author	Jörg Schumacher Volker Behrends Zhensheng Pan Dan R. Brown Franziska Heydenreich Matthew R. Lewis Mark H. Bennett Banafsheh Razzaghi Michal Komorowski Mauricio Barahona Michael P. H. Stumpf Sivaramesh Wigneshweraraj Jacob G. Bundy Martin Buck
author_facet	Jörg Schumacher Volker Behrends Zhensheng Pan Dan R. Brown Franziska Heydenreich Matthew R. Lewis Mark H. Bennett Banafsheh Razzaghi Michal Komorowski Mauricio Barahona Michael P. H. Stumpf Sivaramesh Wigneshweraraj Jacob G. Bundy Martin Buck
author_sort	Jörg Schumacher
title	Nitrogen and Carbon Status Are Integrated at the Transcriptional Level by the Nitrogen Regulator NtrC <italic toggle="yes">In Vivo</italic>
title_short	Nitrogen and Carbon Status Are Integrated at the Transcriptional Level by the Nitrogen Regulator NtrC <italic toggle="yes">In Vivo</italic>
title_full	Nitrogen and Carbon Status Are Integrated at the Transcriptional Level by the Nitrogen Regulator NtrC <italic toggle="yes">In Vivo</italic>
title_fullStr	Nitrogen and Carbon Status Are Integrated at the Transcriptional Level by the Nitrogen Regulator NtrC <italic toggle="yes">In Vivo</italic>
title_full_unstemmed	Nitrogen and Carbon Status Are Integrated at the Transcriptional Level by the Nitrogen Regulator NtrC <italic toggle="yes">In Vivo</italic>
title_sort	nitrogen and carbon status are integrated at the transcriptional level by the nitrogen regulator ntrc <italic toggle="yes">in vivo</italic>
publisher	American Society for Microbiology
publishDate	2013
url	https://doaj.org/article/c6ca6230e20b4eb9b6fba345e8f705e3
work_keys_str_mv	AT jorgschumacher nitrogenandcarbonstatusareintegratedatthetranscriptionallevelbythenitrogenregulatorntrcitalictoggleyesinvivoitalic AT volkerbehrends nitrogenandcarbonstatusareintegratedatthetranscriptionallevelbythenitrogenregulatorntrcitalictoggleyesinvivoitalic AT zhenshengpan nitrogenandcarbonstatusareintegratedatthetranscriptionallevelbythenitrogenregulatorntrcitalictoggleyesinvivoitalic AT danrbrown nitrogenandcarbonstatusareintegratedatthetranscriptionallevelbythenitrogenregulatorntrcitalictoggleyesinvivoitalic AT franziskaheydenreich nitrogenandcarbonstatusareintegratedatthetranscriptionallevelbythenitrogenregulatorntrcitalictoggleyesinvivoitalic AT matthewrlewis nitrogenandcarbonstatusareintegratedatthetranscriptionallevelbythenitrogenregulatorntrcitalictoggleyesinvivoitalic AT markhbennett nitrogenandcarbonstatusareintegratedatthetranscriptionallevelbythenitrogenregulatorntrcitalictoggleyesinvivoitalic AT banafshehrazzaghi nitrogenandcarbonstatusareintegratedatthetranscriptionallevelbythenitrogenregulatorntrcitalictoggleyesinvivoitalic AT michalkomorowski nitrogenandcarbonstatusareintegratedatthetranscriptionallevelbythenitrogenregulatorntrcitalictoggleyesinvivoitalic AT mauriciobarahona nitrogenandcarbonstatusareintegratedatthetranscriptionallevelbythenitrogenregulatorntrcitalictoggleyesinvivoitalic AT michaelphstumpf nitrogenandcarbonstatusareintegratedatthetranscriptionallevelbythenitrogenregulatorntrcitalictoggleyesinvivoitalic AT sivarameshwigneshweraraj nitrogenandcarbonstatusareintegratedatthetranscriptionallevelbythenitrogenregulatorntrcitalictoggleyesinvivoitalic AT jacobgbundy nitrogenandcarbonstatusareintegratedatthetranscriptionallevelbythenitrogenregulatorntrcitalictoggleyesinvivoitalic AT martinbuck nitrogenandcarbonstatusareintegratedatthetranscriptionallevelbythenitrogenregulatorntrcitalictoggleyesinvivoitalic
_version_	1718427611136262144

Nitrogen and Carbon Status Are Integrated at the Transcriptional Level by the Nitrogen Regulator NtrC <italic toggle="yes">In Vivo</italic>

Ejemplares similares