Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus

ABSTRACT Anaerobic gut fungi in the phylum Neocallimastigomycota typically inhabit the digestive tracts of large mammalian herbivores, where they play an integral role in the decomposition of raw lignocellulose into its constitutive sugar monomers. However, quantitative tools to study their physiolo...

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Autores principales:	St. Elmo Wilken, Jonathan M. Monk, Patrick A. Leggieri, Christopher E. Lawson, Thomas S. Lankiewicz, Susanna Seppälä, Chris G. Daum, Jerry Jenkins, Anna M. Lipzen, Stephen J. Mondo, Kerrie W. Barry, Igor V. Grigoriev, John K. Henske, Michael K. Theodorou, Bernhard O. Palsson, Linda R. Petzold, Michelle A. O’Malley
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2021
Materias:	genome-scale metabolic model 13C metabolic flux analysis nonmodel fungus Neocallimastigomycota flux balance analysis Neocallimastix lanati Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/fccac7e8ae6141e8ab56f68f9ad37092
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spelling	oai:doaj.org-article:fccac7e8ae6141e8ab56f68f9ad370922021-12-02T19:22:16ZExperimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus10.1128/mSystems.00002-212379-5077https://doaj.org/article/fccac7e8ae6141e8ab56f68f9ad370922021-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00002-21https://doaj.org/toc/2379-5077ABSTRACT Anaerobic gut fungi in the phylum Neocallimastigomycota typically inhabit the digestive tracts of large mammalian herbivores, where they play an integral role in the decomposition of raw lignocellulose into its constitutive sugar monomers. However, quantitative tools to study their physiology are lacking, partially due to their complex and unresolved metabolism that includes the largely uncharacterized fungal hydrogenosome. Modern omics approaches combined with metabolic modeling can be used to establish an understanding of gut fungal metabolism and develop targeted engineering strategies to harness their degradation capabilities for lignocellulosic bioprocessing. Here, we introduce a high-quality genome of the anaerobic fungus Neocallimastix lanati from which we constructed the first genome-scale metabolic model of an anaerobic fungus. Relative to its size (200 Mbp, sequenced at 62× depth), it is the least fragmented publicly available gut fungal genome to date. Of the 1,788 lignocellulolytic enzymes annotated in the genome, 585 are associated with the fungal cellulosome, underscoring the powerful lignocellulolytic potential of N. lanati. The genome-scale metabolic model captures the primary metabolism of N. lanati and accurately predicts experimentally validated substrate utilization requirements. Additionally, metabolic flux predictions are verified by 13C metabolic flux analysis, demonstrating that the model faithfully describes the underlying fungal metabolism. Furthermore, the model clarifies key aspects of the hydrogenosomal metabolism and can be used as a platform to quantitatively study these biotechnologically important yet poorly understood early-branching fungi. IMPORTANCE Recent genomic analyses have revealed that anaerobic gut fungi possess both the largest number and highest diversity of lignocellulolytic enzymes of all sequenced fungi, explaining their ability to decompose lignocellulosic substrates, e.g., agricultural waste, into fermentable sugars. Despite their potential, the development of engineering methods for these organisms has been slow due to their complex life cycle, understudied metabolism, and challenging anaerobic culture requirements. Currently, there is no framework that can be used to combine multi-omic data sets to understand their physiology. Here, we introduce a high-quality PacBio-sequenced genome of the anaerobic gut fungus Neocallimastix lanati. Beyond identifying a trove of lignocellulolytic enzymes, we use this genome to construct the first genome-scale metabolic model of an anaerobic gut fungus. The model is experimentally validated and sheds light on unresolved metabolic features common to gut fungi. Model-guided analysis will pave the way for deepening our understanding of anaerobic gut fungi and provides a systematic framework to guide strain engineering efforts of these organisms for biotechnological use.St. Elmo WilkenJonathan M. MonkPatrick A. LeggieriChristopher E. LawsonThomas S. LankiewiczSusanna SeppäläChris G. DaumJerry JenkinsAnna M. LipzenStephen J. MondoKerrie W. BarryIgor V. GrigorievJohn K. HenskeMichael K. TheodorouBernhard O. PalssonLinda R. PetzoldMichelle A. O’MalleyAmerican Society for Microbiologyarticlegenome-scale metabolic model13C metabolic flux analysisnonmodel fungusNeocallimastigomycotaflux balance analysisNeocallimastix lanatiMicrobiologyQR1-502ENmSystems, Vol 6, Iss 1 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	genome-scale metabolic model 13C metabolic flux analysis nonmodel fungus Neocallimastigomycota flux balance analysis Neocallimastix lanati Microbiology QR1-502
spellingShingle	genome-scale metabolic model 13C metabolic flux analysis nonmodel fungus Neocallimastigomycota flux balance analysis Neocallimastix lanati Microbiology QR1-502 St. Elmo Wilken Jonathan M. Monk Patrick A. Leggieri Christopher E. Lawson Thomas S. Lankiewicz Susanna Seppälä Chris G. Daum Jerry Jenkins Anna M. Lipzen Stephen J. Mondo Kerrie W. Barry Igor V. Grigoriev John K. Henske Michael K. Theodorou Bernhard O. Palsson Linda R. Petzold Michelle A. O’Malley Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus
description	ABSTRACT Anaerobic gut fungi in the phylum Neocallimastigomycota typically inhabit the digestive tracts of large mammalian herbivores, where they play an integral role in the decomposition of raw lignocellulose into its constitutive sugar monomers. However, quantitative tools to study their physiology are lacking, partially due to their complex and unresolved metabolism that includes the largely uncharacterized fungal hydrogenosome. Modern omics approaches combined with metabolic modeling can be used to establish an understanding of gut fungal metabolism and develop targeted engineering strategies to harness their degradation capabilities for lignocellulosic bioprocessing. Here, we introduce a high-quality genome of the anaerobic fungus Neocallimastix lanati from which we constructed the first genome-scale metabolic model of an anaerobic fungus. Relative to its size (200 Mbp, sequenced at 62× depth), it is the least fragmented publicly available gut fungal genome to date. Of the 1,788 lignocellulolytic enzymes annotated in the genome, 585 are associated with the fungal cellulosome, underscoring the powerful lignocellulolytic potential of N. lanati. The genome-scale metabolic model captures the primary metabolism of N. lanati and accurately predicts experimentally validated substrate utilization requirements. Additionally, metabolic flux predictions are verified by 13C metabolic flux analysis, demonstrating that the model faithfully describes the underlying fungal metabolism. Furthermore, the model clarifies key aspects of the hydrogenosomal metabolism and can be used as a platform to quantitatively study these biotechnologically important yet poorly understood early-branching fungi. IMPORTANCE Recent genomic analyses have revealed that anaerobic gut fungi possess both the largest number and highest diversity of lignocellulolytic enzymes of all sequenced fungi, explaining their ability to decompose lignocellulosic substrates, e.g., agricultural waste, into fermentable sugars. Despite their potential, the development of engineering methods for these organisms has been slow due to their complex life cycle, understudied metabolism, and challenging anaerobic culture requirements. Currently, there is no framework that can be used to combine multi-omic data sets to understand their physiology. Here, we introduce a high-quality PacBio-sequenced genome of the anaerobic gut fungus Neocallimastix lanati. Beyond identifying a trove of lignocellulolytic enzymes, we use this genome to construct the first genome-scale metabolic model of an anaerobic gut fungus. The model is experimentally validated and sheds light on unresolved metabolic features common to gut fungi. Model-guided analysis will pave the way for deepening our understanding of anaerobic gut fungi and provides a systematic framework to guide strain engineering efforts of these organisms for biotechnological use.
format	article
author	St. Elmo Wilken Jonathan M. Monk Patrick A. Leggieri Christopher E. Lawson Thomas S. Lankiewicz Susanna Seppälä Chris G. Daum Jerry Jenkins Anna M. Lipzen Stephen J. Mondo Kerrie W. Barry Igor V. Grigoriev John K. Henske Michael K. Theodorou Bernhard O. Palsson Linda R. Petzold Michelle A. O’Malley
author_facet	St. Elmo Wilken Jonathan M. Monk Patrick A. Leggieri Christopher E. Lawson Thomas S. Lankiewicz Susanna Seppälä Chris G. Daum Jerry Jenkins Anna M. Lipzen Stephen J. Mondo Kerrie W. Barry Igor V. Grigoriev John K. Henske Michael K. Theodorou Bernhard O. Palsson Linda R. Petzold Michelle A. O’Malley
author_sort	St. Elmo Wilken
title	Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus
title_short	Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus
title_full	Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus
title_fullStr	Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus
title_full_unstemmed	Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus
title_sort	experimentally validated reconstruction and analysis of a genome-scale metabolic model of an anaerobic neocallimastigomycota fungus
publisher	American Society for Microbiology
publishDate	2021
url	https://doaj.org/article/fccac7e8ae6141e8ab56f68f9ad37092
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Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus

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