Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine

ABSTRACT Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the...

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Autores principales:	Ritesh Kumar, Suwen Zhao, Matthew W. Vetting, B. McKay Wood, Ayano Sakai, Kyuil Cho, José Solbiati, Steven C. Almo, Jonathan V. Sweedler, Matthew P. Jacobson, John A. Gerlt, John E. Cronan
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2014
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/b13b4ca1a7f9489490ef07a83617a9d7
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spelling	oai:doaj.org-article:b13b4ca1a7f9489490ef07a83617a9d72021-11-15T15:45:11ZPrediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine10.1128/mBio.00933-132150-7511https://doaj.org/article/b13b4ca1a7f9489490ef07a83617a9d72014-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00933-13https://doaj.org/toc/2150-7511ABSTRACT Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catabolic pathway was repressed by osmotic stress and cold stress, and a regulatory transcription factor was identified. We also report crystal structure complexes of the P. denitrificans HpbD hydroxyproline betaine epimerase/proline betaine racemase with l-proline betaine and cis-hydroxyproline betaine. IMPORTANCE At least half of the extant protein annotations are incorrect, and the errors propagate as the number of genome sequences increases exponentially. A large-scale, multidisciplinary sequence- and structure-based strategy for functional assignment of bacterial enzymes of unknown function has demonstrated the pathway for catabolism of the osmoprotectant proline betaine.Ritesh KumarSuwen ZhaoMatthew W. VettingB. McKay WoodAyano SakaiKyuil ChoJosé SolbiatiSteven C. AlmoJonathan V. SweedlerMatthew P. JacobsonJohn A. GerltJohn E. CronanAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 5, Iss 1 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Ritesh Kumar Suwen Zhao Matthew W. Vetting B. McKay Wood Ayano Sakai Kyuil Cho José Solbiati Steven C. Almo Jonathan V. Sweedler Matthew P. Jacobson John A. Gerlt John E. Cronan Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine
description	ABSTRACT Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catabolic pathway was repressed by osmotic stress and cold stress, and a regulatory transcription factor was identified. We also report crystal structure complexes of the P. denitrificans HpbD hydroxyproline betaine epimerase/proline betaine racemase with l-proline betaine and cis-hydroxyproline betaine. IMPORTANCE At least half of the extant protein annotations are incorrect, and the errors propagate as the number of genome sequences increases exponentially. A large-scale, multidisciplinary sequence- and structure-based strategy for functional assignment of bacterial enzymes of unknown function has demonstrated the pathway for catabolism of the osmoprotectant proline betaine.
format	article
author	Ritesh Kumar Suwen Zhao Matthew W. Vetting B. McKay Wood Ayano Sakai Kyuil Cho José Solbiati Steven C. Almo Jonathan V. Sweedler Matthew P. Jacobson John A. Gerlt John E. Cronan
author_facet	Ritesh Kumar Suwen Zhao Matthew W. Vetting B. McKay Wood Ayano Sakai Kyuil Cho José Solbiati Steven C. Almo Jonathan V. Sweedler Matthew P. Jacobson John A. Gerlt John E. Cronan
author_sort	Ritesh Kumar
title	Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine
title_short	Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine
title_full	Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine
title_fullStr	Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine
title_full_unstemmed	Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine
title_sort	prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine
publisher	American Society for Microbiology
publishDate	2014
url	https://doaj.org/article/b13b4ca1a7f9489490ef07a83617a9d7
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Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine

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