A concerted systems biology analysis of phenol metabolism in

Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branched-chain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, we performed 13C-pathway tracing, 13C-pulse-tracing, transcriptional prof...
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Gespeichert in:

Autor*in:	Roell, Garrett W. [verfasserIn] Carr, Rhiannon R. [verfasserIn] Campbell, Tayte [verfasserIn] Shang, Zeyu [verfasserIn] Henson, William R. [verfasserIn] Czajka, Jeffrey J. [verfasserIn] Martín, Hector García [verfasserIn] Zhang, Fuzhong [verfasserIn] Foston, Marcus [verfasserIn] Dantas, Gautam [verfasserIn] Moon, Tae Seok [verfasserIn] Tang, Yinjie J. [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2019

Schlagwörter:	Entner–Doudoroff pathway Gluconeogenesis Lignin

Übergeordnetes Werk:	Enthalten in: Metabolic engineering - Orlando, Fla. : Academic Press, 1999, 55, Seite 120-130
Übergeordnetes Werk:	volume:55 ; pages:120-130

DOI / URN:	10.1016/j.ymben.2019.06.013

Katalog-ID:	ELV002780941

Internformat


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245	1	0	\|a A concerted systems biology analysis of phenol metabolism in
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520			\|a Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branched-chain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, we performed 13C-pathway tracing, 13C-pulse-tracing, transcriptional profiling, biomass composition analysis, and metabolite profiling in conjunction with 13C-metabolic flux analysis (13C-MFA) of phenol metabolism. We found that 1) phenol is metabolized mainly through the ortho–cleavage pathway; 2) phenol utilization requires a highly active TCA cycle; 3) NADPH is generated mainly via NADPH-dependent isocitrate dehydrogenase; 4) active cataplerotic fluxes increase plasticity in the TCA cycle; and 5) gluconeogenesis occurs partially through the reversed Entner–Doudoroff pathway (EDP). We also found that phenol-fed R. opacus PD630 generally has lower sugar phosphate concentrations (e.g., fructose 1,6-bisphosphatase) compared to metabolite pools in 13C-glucose-fed Escherichia coli (set as internal standards), while its TCA metabolites (e.g., malate, succinate, and α-ketoglutarate) accumulate intracellularly with measurable succinate secretion. In addition, we found that phenol utilization was inhibited by benzoate, while catabolite repressions by other tested carbon substrates (e.g., glucose and acetate) were absent in R. opacus PD630. Three adaptively-evolved strains display very different growth rates when fed with phenol as a sole carbon source, but they maintain a conserved flux network. These findings improve our understanding of R. opacus’ metabolism for future lignin valorization.
650		4	\|a Entner–Doudoroff pathway
650		4	\|a Gluconeogenesis
650		4	\|a Lignin
700	1		\|a Carr, Rhiannon R. \|e verfasserin \|4 aut
700	1		\|a Campbell, Tayte \|e verfasserin \|4 aut
700	1		\|a Shang, Zeyu \|e verfasserin \|4 aut
700	1		\|a Henson, William R. \|e verfasserin \|4 aut
700	1		\|a Czajka, Jeffrey J. \|e verfasserin \|4 aut
700	1		\|a Martín, Hector García \|e verfasserin \|4 aut
700	1		\|a Zhang, Fuzhong \|e verfasserin \|4 aut
700	1		\|a Foston, Marcus \|e verfasserin \|4 aut
700	1		\|a Dantas, Gautam \|e verfasserin \|4 aut
700	1		\|a Moon, Tae Seok \|e verfasserin \|4 aut
700	1		\|a Tang, Yinjie J. \|e verfasserin \|4 aut
773	0	8	\|i Enthalten in \|t Metabolic engineering \|d Orlando, Fla. : Academic Press, 1999 \|g 55, Seite 120-130 \|h Online-Ressource \|w (DE-627)267838808 \|w (DE-600)1471017-1 \|w (DE-576)110350340 \|x 1096-7184 \|7 nnns
773	1	8	\|g volume:55 \|g pages:120-130
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912			\|a GBV_ILN_4242
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912			\|a GBV_ILN_4324
912			\|a GBV_ILN_4326
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912			\|a GBV_ILN_4334
912			\|a GBV_ILN_4335
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936	b	k	\|a 42.17 \|j Allgemeine Physiologie \|x Biologie
936	b	k	\|a 42.15 \|j Zellbiologie
951			\|a AR
952			\|d 55 \|h 120-130

Indexfelder

author_variant	g w r gw gwr r r c rr rrc t c tc z s zs w r h wr wrh j j c jj jjc h g m hg hgm f z fz m f mf g d gd t s m ts tsm y j t yj yjt
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publishDate	2019
allfields	10.1016/j.ymben.2019.06.013 doi (DE-627)ELV002780941 (ELSEVIER)S1096-7176(19)30033-3 DE-627 ger DE-627 rda eng 610 DE-600 42.17 bkl 42.15 bkl Roell, Garrett W. verfasserin aut A concerted systems biology analysis of phenol metabolism in 2019 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branched-chain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, we performed 13C-pathway tracing, 13C-pulse-tracing, transcriptional profiling, biomass composition analysis, and metabolite profiling in conjunction with 13C-metabolic flux analysis (13C-MFA) of phenol metabolism. We found that 1) phenol is metabolized mainly through the ortho–cleavage pathway; 2) phenol utilization requires a highly active TCA cycle; 3) NADPH is generated mainly via NADPH-dependent isocitrate dehydrogenase; 4) active cataplerotic fluxes increase plasticity in the TCA cycle; and 5) gluconeogenesis occurs partially through the reversed Entner–Doudoroff pathway (EDP). We also found that phenol-fed R. opacus PD630 generally has lower sugar phosphate concentrations (e.g., fructose 1,6-bisphosphatase) compared to metabolite pools in 13C-glucose-fed Escherichia coli (set as internal standards), while its TCA metabolites (e.g., malate, succinate, and α-ketoglutarate) accumulate intracellularly with measurable succinate secretion. In addition, we found that phenol utilization was inhibited by benzoate, while catabolite repressions by other tested carbon substrates (e.g., glucose and acetate) were absent in R. opacus PD630. Three adaptively-evolved strains display very different growth rates when fed with phenol as a sole carbon source, but they maintain a conserved flux network. These findings improve our understanding of R. opacus’ metabolism for future lignin valorization. Entner–Doudoroff pathway Gluconeogenesis Lignin Carr, Rhiannon R. verfasserin aut Campbell, Tayte verfasserin aut Shang, Zeyu verfasserin aut Henson, William R. verfasserin aut Czajka, Jeffrey J. verfasserin aut Martín, Hector García verfasserin aut Zhang, Fuzhong verfasserin aut Foston, Marcus verfasserin aut Dantas, Gautam verfasserin aut Moon, Tae Seok verfasserin aut Tang, Yinjie J. verfasserin aut Enthalten in Metabolic engineering Orlando, Fla. : Academic Press, 1999 55, Seite 120-130 Online-Ressource (DE-627)267838808 (DE-600)1471017-1 (DE-576)110350340 1096-7184 nnns volume:55 pages:120-130 GBV_USEFLAG_U SYSFLAG_U GBV_ELV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_150 GBV_ILN_151 GBV_ILN_165 GBV_ILN_224 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4393 42.17 Allgemeine Physiologie Biologie 42.15 Zellbiologie AR 55 120-130
spelling	10.1016/j.ymben.2019.06.013 doi (DE-627)ELV002780941 (ELSEVIER)S1096-7176(19)30033-3 DE-627 ger DE-627 rda eng 610 DE-600 42.17 bkl 42.15 bkl Roell, Garrett W. verfasserin aut A concerted systems biology analysis of phenol metabolism in 2019 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branched-chain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, we performed 13C-pathway tracing, 13C-pulse-tracing, transcriptional profiling, biomass composition analysis, and metabolite profiling in conjunction with 13C-metabolic flux analysis (13C-MFA) of phenol metabolism. We found that 1) phenol is metabolized mainly through the ortho–cleavage pathway; 2) phenol utilization requires a highly active TCA cycle; 3) NADPH is generated mainly via NADPH-dependent isocitrate dehydrogenase; 4) active cataplerotic fluxes increase plasticity in the TCA cycle; and 5) gluconeogenesis occurs partially through the reversed Entner–Doudoroff pathway (EDP). We also found that phenol-fed R. opacus PD630 generally has lower sugar phosphate concentrations (e.g., fructose 1,6-bisphosphatase) compared to metabolite pools in 13C-glucose-fed Escherichia coli (set as internal standards), while its TCA metabolites (e.g., malate, succinate, and α-ketoglutarate) accumulate intracellularly with measurable succinate secretion. In addition, we found that phenol utilization was inhibited by benzoate, while catabolite repressions by other tested carbon substrates (e.g., glucose and acetate) were absent in R. opacus PD630. Three adaptively-evolved strains display very different growth rates when fed with phenol as a sole carbon source, but they maintain a conserved flux network. These findings improve our understanding of R. opacus’ metabolism for future lignin valorization. Entner–Doudoroff pathway Gluconeogenesis Lignin Carr, Rhiannon R. verfasserin aut Campbell, Tayte verfasserin aut Shang, Zeyu verfasserin aut Henson, William R. verfasserin aut Czajka, Jeffrey J. verfasserin aut Martín, Hector García verfasserin aut Zhang, Fuzhong verfasserin aut Foston, Marcus verfasserin aut Dantas, Gautam verfasserin aut Moon, Tae Seok verfasserin aut Tang, Yinjie J. verfasserin aut Enthalten in Metabolic engineering Orlando, Fla. : Academic Press, 1999 55, Seite 120-130 Online-Ressource (DE-627)267838808 (DE-600)1471017-1 (DE-576)110350340 1096-7184 nnns volume:55 pages:120-130 GBV_USEFLAG_U SYSFLAG_U GBV_ELV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_150 GBV_ILN_151 GBV_ILN_165 GBV_ILN_224 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4393 42.17 Allgemeine Physiologie Biologie 42.15 Zellbiologie AR 55 120-130
allfields_unstemmed	10.1016/j.ymben.2019.06.013 doi (DE-627)ELV002780941 (ELSEVIER)S1096-7176(19)30033-3 DE-627 ger DE-627 rda eng 610 DE-600 42.17 bkl 42.15 bkl Roell, Garrett W. verfasserin aut A concerted systems biology analysis of phenol metabolism in 2019 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branched-chain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, we performed 13C-pathway tracing, 13C-pulse-tracing, transcriptional profiling, biomass composition analysis, and metabolite profiling in conjunction with 13C-metabolic flux analysis (13C-MFA) of phenol metabolism. We found that 1) phenol is metabolized mainly through the ortho–cleavage pathway; 2) phenol utilization requires a highly active TCA cycle; 3) NADPH is generated mainly via NADPH-dependent isocitrate dehydrogenase; 4) active cataplerotic fluxes increase plasticity in the TCA cycle; and 5) gluconeogenesis occurs partially through the reversed Entner–Doudoroff pathway (EDP). We also found that phenol-fed R. opacus PD630 generally has lower sugar phosphate concentrations (e.g., fructose 1,6-bisphosphatase) compared to metabolite pools in 13C-glucose-fed Escherichia coli (set as internal standards), while its TCA metabolites (e.g., malate, succinate, and α-ketoglutarate) accumulate intracellularly with measurable succinate secretion. In addition, we found that phenol utilization was inhibited by benzoate, while catabolite repressions by other tested carbon substrates (e.g., glucose and acetate) were absent in R. opacus PD630. Three adaptively-evolved strains display very different growth rates when fed with phenol as a sole carbon source, but they maintain a conserved flux network. These findings improve our understanding of R. opacus’ metabolism for future lignin valorization. Entner–Doudoroff pathway Gluconeogenesis Lignin Carr, Rhiannon R. verfasserin aut Campbell, Tayte verfasserin aut Shang, Zeyu verfasserin aut Henson, William R. verfasserin aut Czajka, Jeffrey J. verfasserin aut Martín, Hector García verfasserin aut Zhang, Fuzhong verfasserin aut Foston, Marcus verfasserin aut Dantas, Gautam verfasserin aut Moon, Tae Seok verfasserin aut Tang, Yinjie J. verfasserin aut Enthalten in Metabolic engineering Orlando, Fla. : Academic Press, 1999 55, Seite 120-130 Online-Ressource (DE-627)267838808 (DE-600)1471017-1 (DE-576)110350340 1096-7184 nnns volume:55 pages:120-130 GBV_USEFLAG_U SYSFLAG_U GBV_ELV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_150 GBV_ILN_151 GBV_ILN_165 GBV_ILN_224 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4393 42.17 Allgemeine Physiologie Biologie 42.15 Zellbiologie AR 55 120-130
allfieldsGer	10.1016/j.ymben.2019.06.013 doi (DE-627)ELV002780941 (ELSEVIER)S1096-7176(19)30033-3 DE-627 ger DE-627 rda eng 610 DE-600 42.17 bkl 42.15 bkl Roell, Garrett W. verfasserin aut A concerted systems biology analysis of phenol metabolism in 2019 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branched-chain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, we performed 13C-pathway tracing, 13C-pulse-tracing, transcriptional profiling, biomass composition analysis, and metabolite profiling in conjunction with 13C-metabolic flux analysis (13C-MFA) of phenol metabolism. We found that 1) phenol is metabolized mainly through the ortho–cleavage pathway; 2) phenol utilization requires a highly active TCA cycle; 3) NADPH is generated mainly via NADPH-dependent isocitrate dehydrogenase; 4) active cataplerotic fluxes increase plasticity in the TCA cycle; and 5) gluconeogenesis occurs partially through the reversed Entner–Doudoroff pathway (EDP). We also found that phenol-fed R. opacus PD630 generally has lower sugar phosphate concentrations (e.g., fructose 1,6-bisphosphatase) compared to metabolite pools in 13C-glucose-fed Escherichia coli (set as internal standards), while its TCA metabolites (e.g., malate, succinate, and α-ketoglutarate) accumulate intracellularly with measurable succinate secretion. In addition, we found that phenol utilization was inhibited by benzoate, while catabolite repressions by other tested carbon substrates (e.g., glucose and acetate) were absent in R. opacus PD630. Three adaptively-evolved strains display very different growth rates when fed with phenol as a sole carbon source, but they maintain a conserved flux network. These findings improve our understanding of R. opacus’ metabolism for future lignin valorization. Entner–Doudoroff pathway Gluconeogenesis Lignin Carr, Rhiannon R. verfasserin aut Campbell, Tayte verfasserin aut Shang, Zeyu verfasserin aut Henson, William R. verfasserin aut Czajka, Jeffrey J. verfasserin aut Martín, Hector García verfasserin aut Zhang, Fuzhong verfasserin aut Foston, Marcus verfasserin aut Dantas, Gautam verfasserin aut Moon, Tae Seok verfasserin aut Tang, Yinjie J. verfasserin aut Enthalten in Metabolic engineering Orlando, Fla. : Academic Press, 1999 55, Seite 120-130 Online-Ressource (DE-627)267838808 (DE-600)1471017-1 (DE-576)110350340 1096-7184 nnns volume:55 pages:120-130 GBV_USEFLAG_U SYSFLAG_U GBV_ELV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_150 GBV_ILN_151 GBV_ILN_165 GBV_ILN_224 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4393 42.17 Allgemeine Physiologie Biologie 42.15 Zellbiologie AR 55 120-130
allfieldsSound	10.1016/j.ymben.2019.06.013 doi (DE-627)ELV002780941 (ELSEVIER)S1096-7176(19)30033-3 DE-627 ger DE-627 rda eng 610 DE-600 42.17 bkl 42.15 bkl Roell, Garrett W. verfasserin aut A concerted systems biology analysis of phenol metabolism in 2019 nicht spezifiziert zzz rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branched-chain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, we performed 13C-pathway tracing, 13C-pulse-tracing, transcriptional profiling, biomass composition analysis, and metabolite profiling in conjunction with 13C-metabolic flux analysis (13C-MFA) of phenol metabolism. We found that 1) phenol is metabolized mainly through the ortho–cleavage pathway; 2) phenol utilization requires a highly active TCA cycle; 3) NADPH is generated mainly via NADPH-dependent isocitrate dehydrogenase; 4) active cataplerotic fluxes increase plasticity in the TCA cycle; and 5) gluconeogenesis occurs partially through the reversed Entner–Doudoroff pathway (EDP). We also found that phenol-fed R. opacus PD630 generally has lower sugar phosphate concentrations (e.g., fructose 1,6-bisphosphatase) compared to metabolite pools in 13C-glucose-fed Escherichia coli (set as internal standards), while its TCA metabolites (e.g., malate, succinate, and α-ketoglutarate) accumulate intracellularly with measurable succinate secretion. In addition, we found that phenol utilization was inhibited by benzoate, while catabolite repressions by other tested carbon substrates (e.g., glucose and acetate) were absent in R. opacus PD630. Three adaptively-evolved strains display very different growth rates when fed with phenol as a sole carbon source, but they maintain a conserved flux network. These findings improve our understanding of R. opacus’ metabolism for future lignin valorization. Entner–Doudoroff pathway Gluconeogenesis Lignin Carr, Rhiannon R. verfasserin aut Campbell, Tayte verfasserin aut Shang, Zeyu verfasserin aut Henson, William R. verfasserin aut Czajka, Jeffrey J. verfasserin aut Martín, Hector García verfasserin aut Zhang, Fuzhong verfasserin aut Foston, Marcus verfasserin aut Dantas, Gautam verfasserin aut Moon, Tae Seok verfasserin aut Tang, Yinjie J. verfasserin aut Enthalten in Metabolic engineering Orlando, Fla. : Academic Press, 1999 55, Seite 120-130 Online-Ressource (DE-627)267838808 (DE-600)1471017-1 (DE-576)110350340 1096-7184 nnns volume:55 pages:120-130 GBV_USEFLAG_U SYSFLAG_U GBV_ELV SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_150 GBV_ILN_151 GBV_ILN_165 GBV_ILN_224 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4393 42.17 Allgemeine Physiologie Biologie 42.15 Zellbiologie AR 55 120-130
language	English
source	Enthalten in Metabolic engineering 55, Seite 120-130 volume:55 pages:120-130
sourceStr	Enthalten in Metabolic engineering 55, Seite 120-130 volume:55 pages:120-130
format_phy_str_mv	Article
bklname	Allgemeine Physiologie Zellbiologie
institution	findex.gbv.de
topic_facet	Entner–Doudoroff pathway Gluconeogenesis Lignin
dewey-raw	610
isfreeaccess_bool	false
container_title	Metabolic engineering
authorswithroles_txt_mv	Roell, Garrett W. @@aut@@ Carr, Rhiannon R. @@aut@@ Campbell, Tayte @@aut@@ Shang, Zeyu @@aut@@ Henson, William R. @@aut@@ Czajka, Jeffrey J. @@aut@@ Martín, Hector García @@aut@@ Zhang, Fuzhong @@aut@@ Foston, Marcus @@aut@@ Dantas, Gautam @@aut@@ Moon, Tae Seok @@aut@@ Tang, Yinjie J. @@aut@@
publishDateDaySort_date	2019-01-01T00:00:00Z
hierarchy_top_id	267838808
dewey-sort	3610
id	ELV002780941
language_de	englisch
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author	Roell, Garrett W.
spellingShingle	Roell, Garrett W. ddc 610 bkl 42.17 bkl 42.15 misc Entner–Doudoroff pathway misc Gluconeogenesis misc Lignin A concerted systems biology analysis of phenol metabolism in
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topic_title	610 DE-600 42.17 bkl 42.15 bkl A concerted systems biology analysis of phenol metabolism in Entner–Doudoroff pathway Gluconeogenesis Lignin
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title	A concerted systems biology analysis of phenol metabolism in
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title_full	A concerted systems biology analysis of phenol metabolism in
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author_browse	Roell, Garrett W. Carr, Rhiannon R. Campbell, Tayte Shang, Zeyu Henson, William R. Czajka, Jeffrey J. Martín, Hector García Zhang, Fuzhong Foston, Marcus Dantas, Gautam Moon, Tae Seok Tang, Yinjie J.
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title_sort	a concerted systems biology analysis of phenol metabolism in
title_auth	A concerted systems biology analysis of phenol metabolism in
abstract	Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branched-chain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, we performed 13C-pathway tracing, 13C-pulse-tracing, transcriptional profiling, biomass composition analysis, and metabolite profiling in conjunction with 13C-metabolic flux analysis (13C-MFA) of phenol metabolism. We found that 1) phenol is metabolized mainly through the ortho–cleavage pathway; 2) phenol utilization requires a highly active TCA cycle; 3) NADPH is generated mainly via NADPH-dependent isocitrate dehydrogenase; 4) active cataplerotic fluxes increase plasticity in the TCA cycle; and 5) gluconeogenesis occurs partially through the reversed Entner–Doudoroff pathway (EDP). We also found that phenol-fed R. opacus PD630 generally has lower sugar phosphate concentrations (e.g., fructose 1,6-bisphosphatase) compared to metabolite pools in 13C-glucose-fed Escherichia coli (set as internal standards), while its TCA metabolites (e.g., malate, succinate, and α-ketoglutarate) accumulate intracellularly with measurable succinate secretion. In addition, we found that phenol utilization was inhibited by benzoate, while catabolite repressions by other tested carbon substrates (e.g., glucose and acetate) were absent in R. opacus PD630. Three adaptively-evolved strains display very different growth rates when fed with phenol as a sole carbon source, but they maintain a conserved flux network. These findings improve our understanding of R. opacus’ metabolism for future lignin valorization.
abstractGer	Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branched-chain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, we performed 13C-pathway tracing, 13C-pulse-tracing, transcriptional profiling, biomass composition analysis, and metabolite profiling in conjunction with 13C-metabolic flux analysis (13C-MFA) of phenol metabolism. We found that 1) phenol is metabolized mainly through the ortho–cleavage pathway; 2) phenol utilization requires a highly active TCA cycle; 3) NADPH is generated mainly via NADPH-dependent isocitrate dehydrogenase; 4) active cataplerotic fluxes increase plasticity in the TCA cycle; and 5) gluconeogenesis occurs partially through the reversed Entner–Doudoroff pathway (EDP). We also found that phenol-fed R. opacus PD630 generally has lower sugar phosphate concentrations (e.g., fructose 1,6-bisphosphatase) compared to metabolite pools in 13C-glucose-fed Escherichia coli (set as internal standards), while its TCA metabolites (e.g., malate, succinate, and α-ketoglutarate) accumulate intracellularly with measurable succinate secretion. In addition, we found that phenol utilization was inhibited by benzoate, while catabolite repressions by other tested carbon substrates (e.g., glucose and acetate) were absent in R. opacus PD630. Three adaptively-evolved strains display very different growth rates when fed with phenol as a sole carbon source, but they maintain a conserved flux network. These findings improve our understanding of R. opacus’ metabolism for future lignin valorization.
abstract_unstemmed	Rhodococcus opacus PD630 metabolizes aromatic substrates and naturally produces branched-chain lipids, which are advantageous traits for lignin valorization. To provide insights into its lignocellulose hydrolysate utilization, we performed 13C-pathway tracing, 13C-pulse-tracing, transcriptional profiling, biomass composition analysis, and metabolite profiling in conjunction with 13C-metabolic flux analysis (13C-MFA) of phenol metabolism. We found that 1) phenol is metabolized mainly through the ortho–cleavage pathway; 2) phenol utilization requires a highly active TCA cycle; 3) NADPH is generated mainly via NADPH-dependent isocitrate dehydrogenase; 4) active cataplerotic fluxes increase plasticity in the TCA cycle; and 5) gluconeogenesis occurs partially through the reversed Entner–Doudoroff pathway (EDP). We also found that phenol-fed R. opacus PD630 generally has lower sugar phosphate concentrations (e.g., fructose 1,6-bisphosphatase) compared to metabolite pools in 13C-glucose-fed Escherichia coli (set as internal standards), while its TCA metabolites (e.g., malate, succinate, and α-ketoglutarate) accumulate intracellularly with measurable succinate secretion. In addition, we found that phenol utilization was inhibited by benzoate, while catabolite repressions by other tested carbon substrates (e.g., glucose and acetate) were absent in R. opacus PD630. Three adaptively-evolved strains display very different growth rates when fed with phenol as a sole carbon source, but they maintain a conserved flux network. These findings improve our understanding of R. opacus’ metabolism for future lignin valorization.
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title_short	A concerted systems biology analysis of phenol metabolism in
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author2	Carr, Rhiannon R. Campbell, Tayte Shang, Zeyu Henson, William R. Czajka, Jeffrey J. Martín, Hector García Zhang, Fuzhong Foston, Marcus Dantas, Gautam Moon, Tae Seok Tang, Yinjie J.
author2Str	Carr, Rhiannon R. Campbell, Tayte Shang, Zeyu Henson, William R. Czajka, Jeffrey J. Martín, Hector García Zhang, Fuzhong Foston, Marcus Dantas, Gautam Moon, Tae Seok Tang, Yinjie J.
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To provide insights into its lignocellulose hydrolysate utilization, we performed 13C-pathway tracing, 13C-pulse-tracing, transcriptional profiling, biomass composition analysis, and metabolite profiling in conjunction with 13C-metabolic flux analysis (13C-MFA) of phenol metabolism. We found that 1) phenol is metabolized mainly through the ortho–cleavage pathway; 2) phenol utilization requires a highly active TCA cycle; 3) NADPH is generated mainly via NADPH-dependent isocitrate dehydrogenase; 4) active cataplerotic fluxes increase plasticity in the TCA cycle; and 5) gluconeogenesis occurs partially through the reversed Entner–Doudoroff pathway (EDP). We also found that phenol-fed R. opacus PD630 generally has lower sugar phosphate concentrations (e.g., fructose 1,6-bisphosphatase) compared to metabolite pools in 13C-glucose-fed Escherichia coli (set as internal standards), while its TCA metabolites (e.g., malate, succinate, and α-ketoglutarate) accumulate intracellularly with measurable succinate secretion. In addition, we found that phenol utilization was inhibited by benzoate, while catabolite repressions by other tested carbon substrates (e.g., glucose and acetate) were absent in R. opacus PD630. Three adaptively-evolved strains display very different growth rates when fed with phenol as a sole carbon source, but they maintain a conserved flux network. These findings improve our understanding of R. opacus’ metabolism for future lignin valorization.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Entner–Doudoroff pathway</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Gluconeogenesis</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Lignin</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Carr, Rhiannon R.</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Campbell, Tayte</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Shang, Zeyu</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Henson, William 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