Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph <italic toggle="yes">Methylomicrobium buryatense</italic> 5GB1

ABSTRACT Methylomicrobium buryatense 5GB1 is an obligate methylotroph which grows on methane or methanol with similar growth rates. It has long been assumed that the core metabolic pathways must be similar on the two substrates, but recent studies of methane metabolism in this bacterium suggest that...

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Autores principales:	Yanfen Fu, Lian He, Jennifer Reeve, David A. C. Beck, Mary E. Lidstrom
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	13C tracer analysis flux balance analysis methanol methanotrophs Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/afd423e0ece4447493666c5c90788a74
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spelling	oai:doaj.org-article:afd423e0ece4447493666c5c90788a742021-11-15T15:55:25ZCore Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph <italic toggle="yes">Methylomicrobium buryatense</italic> 5GB110.1128/mBio.00406-192150-7511https://doaj.org/article/afd423e0ece4447493666c5c90788a742019-04-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00406-19https://doaj.org/toc/2150-7511ABSTRACT Methylomicrobium buryatense 5GB1 is an obligate methylotroph which grows on methane or methanol with similar growth rates. It has long been assumed that the core metabolic pathways must be similar on the two substrates, but recent studies of methane metabolism in this bacterium suggest that growth on methanol might have significant differences from growth on methane. In this study, both a targeted metabolomics approach and a 13C tracer approach were taken to understand core carbon metabolism in M. buryatense 5GB1 during growth on methanol and to determine whether such differences occur. Our results suggest a systematic shift of active core metabolism in which increased flux occurred through both the Entner-Doudoroff (ED) pathway and the partial serine cycle, while the tricarboxylic acid (TCA) cycle was incomplete, in contrast to growth on methane. Using the experimental results as constraints, we applied flux balance analysis to determine the metabolic flux phenotype of M. buryatense 5GB1 growing on methanol, and the results are consistent with predictions based on ATP and NADH changes. Transcriptomics analysis suggested that the changes in fluxes and metabolite levels represented results of posttranscriptional regulation. The combination of flux balance analysis of the genome-scale model and the flux ratio from 13C data changed the solution space for a better prediction of cell behavior and demonstrated the significant differences in physiology between growth on methane and growth on methanol. IMPORTANCE One-carbon compounds such as methane and methanol are of increasing interest as sustainable substrates for biological production of fuels and industrial chemicals. The bacteria that carry out these conversions have been studied for many decades, but gaps exist in our knowledge of their metabolic pathways. One such gap is the difference between growth on methane and growth on methanol. Understanding such metabolism is important, since each has advantages and disadvantages as a feedstock for production of chemicals and fuels. The significance of our research is in the demonstration that the metabolic network is substantially altered in each case and in the delineation of these changes. The resulting new insights into the core metabolism of this bacterium now provide an improved basis for future strain design.Yanfen FuLian HeJennifer ReeveDavid A. C. BeckMary E. LidstromAmerican Society for Microbiologyarticle13C tracer analysisflux balance analysismethanolmethanotrophsMicrobiologyQR1-502ENmBio, Vol 10, Iss 2 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	13C tracer analysis flux balance analysis methanol methanotrophs Microbiology QR1-502
spellingShingle	13C tracer analysis flux balance analysis methanol methanotrophs Microbiology QR1-502 Yanfen Fu Lian He Jennifer Reeve David A. C. Beck Mary E. Lidstrom Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph <italic toggle="yes">Methylomicrobium buryatense</italic> 5GB1
description	ABSTRACT Methylomicrobium buryatense 5GB1 is an obligate methylotroph which grows on methane or methanol with similar growth rates. It has long been assumed that the core metabolic pathways must be similar on the two substrates, but recent studies of methane metabolism in this bacterium suggest that growth on methanol might have significant differences from growth on methane. In this study, both a targeted metabolomics approach and a 13C tracer approach were taken to understand core carbon metabolism in M. buryatense 5GB1 during growth on methanol and to determine whether such differences occur. Our results suggest a systematic shift of active core metabolism in which increased flux occurred through both the Entner-Doudoroff (ED) pathway and the partial serine cycle, while the tricarboxylic acid (TCA) cycle was incomplete, in contrast to growth on methane. Using the experimental results as constraints, we applied flux balance analysis to determine the metabolic flux phenotype of M. buryatense 5GB1 growing on methanol, and the results are consistent with predictions based on ATP and NADH changes. Transcriptomics analysis suggested that the changes in fluxes and metabolite levels represented results of posttranscriptional regulation. The combination of flux balance analysis of the genome-scale model and the flux ratio from 13C data changed the solution space for a better prediction of cell behavior and demonstrated the significant differences in physiology between growth on methane and growth on methanol. IMPORTANCE One-carbon compounds such as methane and methanol are of increasing interest as sustainable substrates for biological production of fuels and industrial chemicals. The bacteria that carry out these conversions have been studied for many decades, but gaps exist in our knowledge of their metabolic pathways. One such gap is the difference between growth on methane and growth on methanol. Understanding such metabolism is important, since each has advantages and disadvantages as a feedstock for production of chemicals and fuels. The significance of our research is in the demonstration that the metabolic network is substantially altered in each case and in the delineation of these changes. The resulting new insights into the core metabolism of this bacterium now provide an improved basis for future strain design.
format	article
author	Yanfen Fu Lian He Jennifer Reeve David A. C. Beck Mary E. Lidstrom
author_facet	Yanfen Fu Lian He Jennifer Reeve David A. C. Beck Mary E. Lidstrom
author_sort	Yanfen Fu
title	Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph <italic toggle="yes">Methylomicrobium buryatense</italic> 5GB1
title_short	Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph <italic toggle="yes">Methylomicrobium buryatense</italic> 5GB1
title_full	Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph <italic toggle="yes">Methylomicrobium buryatense</italic> 5GB1
title_fullStr	Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph <italic toggle="yes">Methylomicrobium buryatense</italic> 5GB1
title_full_unstemmed	Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph <italic toggle="yes">Methylomicrobium buryatense</italic> 5GB1
title_sort	core metabolism shifts during growth on methanol versus methane in the methanotroph <italic toggle="yes">methylomicrobium buryatense</italic> 5gb1
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/afd423e0ece4447493666c5c90788a74
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Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph <italic toggle="yes">Methylomicrobium buryatense</italic> 5GB1

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