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Article ; Online: Consolidated bioprocessing of plant biomass to polyhydroxyalkanoate by co-culture of Streptomyces sp. SirexAA-E and Priestia megaterium.

Kumar, Vijay / Fox, Brian G / Takasuka, Taichi E

2023 Volume 376, Page(s) 128934

Abstract: Polyhydroxyalkanoate (PHA) production from plant biomass is an ideal way to realize sustainable PHA-based bioplastic. The present study demonstrated consolidated bioconversion of plant biomass to PHA by co-culturing two specialized bacteria, cellulolytic ...

Abstract	Polyhydroxyalkanoate (PHA) production from plant biomass is an ideal way to realize sustainable PHA-based bioplastic. The present study demonstrated consolidated bioconversion of plant biomass to PHA by co-culturing two specialized bacteria, cellulolytic Streptomyces sp. SirexAA-E and PHA producing Priestia megaterium. In monoculture, S. sp. SirexAA-E does not produce PHA, while P. megaterium did not grow on plant polysaccharides. The co-culture showed poly(3-hydroxybutyrate) (PHB) production using purified polysaccharides, including cellulose, xylan, mannan and their combinations, and plant biomass (Miscanthus, corn stalk and corn leaves) as sole carbon sources, confirmed by GC-MS. The co-culture inoculated with 1:4 (v/v) ratio of S. sp. SirexAA-E to P. megaterium produced 40 mg PHB/g Miscanthus using 0.5% biomass loading. Realtime PCR showed ∼85% S. sp. SirexAA-E and ∼15% P. megaterium in the co-culture. Thus, this study provides a concept of proof for one-pot bioconversion of plant biomass into PHB without separate saccharification processes.
MeSH term(s)	Polyhydroxyalkanoates ; Biomass ; Streptomyces/genetics ; Coculture Techniques ; Plants ; Polysaccharides ; Poaceae
Chemical Substances	Polyhydroxyalkanoates ; Polysaccharides
Language	English
Publishing date	2023-03-20
Publishing country	England
Document type	Journal Article
ZDB-ID	1065195-0
ISSN	1873-2976 ; 0960-8524
ISSN (online)	1873-2976
ISSN	0960-8524
DOI	10.1016/j.biortech.2023.128934
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Article ; Online: Consolidated bioprocessing of plant biomass to polyhydroxyalkanoate by co-culture of Streptomyces sp. SirexAA-E and Priestia megaterium

Kumar, Vijay / Fox, Brian G. / Takasuka, Taichi E.

Bioresource Technology. 2023 May, v. 376 p.128934-

2023

Abstract	Polyhydroxyalkanoate (PHA) production from plant biomass is an ideal way to realize sustainable PHA-based bioplastic. The present study demonstrated consolidated bioconversion of plant biomass to PHA by co-culturing two specialized bacteria, cellulolytic Streptomyces sp. SirexAA-E and PHA producing Priestia megaterium. In monoculture, S. sp. SirexAA-E does not produce PHA, while P. megaterium did not grow on plant polysaccharides. The co-culture showed poly(3-hydroxybutyrate) (PHB) production using purified polysaccharides, including cellulose, xylan, mannan and their combinations, and plant biomass (Miscanthus, corn stalk and corn leaves) as sole carbon sources, confirmed by GC–MS. The co-culture inoculated with 1:4 (v/v) ratio of S. sp. SirexAA-E to P. megaterium produced 40 mg PHB/g Miscanthus using 0.5% biomass loading. Realtime PCR showed ∼85% S. sp. SirexAA-E and ∼15% P. megaterium in the co-culture. Thus, this study provides a concept of proof for one-pot bioconversion of plant biomass into PHB without separate saccharification processes.
Keywords	Miscanthus ; Streptomyces ; bioplastics ; bioprocessing ; biotransformation ; carbon ; cellulose ; coculture ; corn ; corn stover ; phytomass ; polyhydroxyalkanoates ; quantitative polymerase chain reaction ; saccharification ; xylan ; Biomass ; Synthetic consortium ; Consolidated bioprocess ; Polyhydroxyalkanoate
Language	English
Dates of publication	2023-05
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	1065195-0
ISSN	1873-2976 ; 0960-8524
ISSN (online)	1873-2976
ISSN	0960-8524
DOI	10.1016/j.biortech.2023.128934
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Article ; Online: A Single DNA Point Mutation Leads to the Formation of a Cysteine-Tyrosine Crosslink in the Cysteine Dioxygenase from

Schultz, Rebecca L / Sabat, Grzegorz / Fox, Brian G / Brunold, Thomas C

Biochemistry

2023 Volume 62, Issue 12, Page(s) 1964–1975

Abstract: Cysteine dioxygenase (CDO) is a non-heme iron-containing enzyme that catalyzes the oxidation of cysteine (Cys) to cysteine sulfinic acid (CSA). Crystal structures of eukaryotic CDOs revealed the presence of an unusual crosslink between the sulfur of a ... ...

Abstract	Cysteine dioxygenase (CDO) is a non-heme iron-containing enzyme that catalyzes the oxidation of cysteine (Cys) to cysteine sulfinic acid (CSA). Crystal structures of eukaryotic CDOs revealed the presence of an unusual crosslink between the sulfur of a cysteine residue (C93 in
MeSH term(s)	Animals ; Mice ; Bacillus subtilis/genetics ; Bacillus subtilis/metabolism ; Cysteine/genetics ; Cysteine Dioxygenase/chemistry ; Cysteine Dioxygenase/genetics ; Kinetics ; Point Mutation ; Tyrosine/genetics
Chemical Substances	Cysteine (K848JZ4886) ; Cysteine Dioxygenase (EC 1.13.11.20) ; Tyrosine (42HK56048U)
Language	English
Publishing date	2023-06-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.3c00083
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Article ; Online: Predicting individual differences in motor learning: A critical review.

Ranganathan, Rajiv / Cone, Simon / Fox, Brian

Neuroscience and biobehavioral reviews

2022 Volume 141, Page(s) 104852

Abstract: The ability to predict individual differences in motor learning has significant implications from both theoretical and applied perspectives. However, there is high variability in the methodological and analytical strategies employed as evidence for such ... ...

Abstract	The ability to predict individual differences in motor learning has significant implications from both theoretical and applied perspectives. However, there is high variability in the methodological and analytical strategies employed as evidence for such predictions. Here, we critically examine the evidence for predictions of individual differences in motor learning by reviewing the literature from a 20-year period (2000-2020). Specifically, we examined four factors: (i) the predictor and predicted variables used, (ii) the strength of the prediction and associated sample size, (iii) the timescale over which the prediction was made, and (iv) the type of motor task used. Overall, the results highlight several issues that raise concerns about the quality of the evidence for such predictions. First, there was a large variation in both predictor and predicted variables, suggesting the presence of a large number of researcher degrees of freedom. Second, sample sizes tended to be small, and the strength of the correlation showed an inverse relation with sample size. Third, the timescale of most predictions was very short, mostly constrained to a single day. Last, most studies were largely restricted to two experimental paradigms - adaptation and sequence learning. Based on these issues, we highlight recommendations for future studies to improve the quality of evidence for predicting individual differences in motor learning.
MeSH term(s)	Adaptation, Physiological ; Humans ; Individuality ; Learning
Language	English
Publishing date	2022-09-01
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	282464-4
ISSN	1873-7528 ; 0149-7634
ISSN (online)	1873-7528
ISSN	0149-7634
DOI	10.1016/j.neubiorev.2022.104852
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Article ; Online: Contribution of calcium ligands in substrate binding and product release in the Acetovibrio thermocellus glycoside hydrolase family 9 cellulase CelR.

Kuch, Nathaniel J / Kutschke, Mark E / Parker, Alex / Bingman, Craig A / Fox, Brian G

The Journal of biological chemistry

2023 Volume 299, Issue 5, Page(s) 104655

Abstract: Enzymatic deconstruction of lignocellulosic biomass is crucial to establishment of the renewable biofuel and bioproduct economy. Better understanding of these enzymes, including their catalytic and binding domains, and other features offer potential ... ...

Abstract	Enzymatic deconstruction of lignocellulosic biomass is crucial to establishment of the renewable biofuel and bioproduct economy. Better understanding of these enzymes, including their catalytic and binding domains, and other features offer potential avenues for improvement. Glycoside hydrolase family 9 (GH9) enzymes are attractive targets because they have members that exhibit exo- and endo-cellulolytic activity, processivity of reaction, and thermostability. This study examines a GH9 from Acetovibrio thermocellus ATCC 27405, AtCelR containing a catalytic domain and a carbohydrate binding module (CBM3c). Crystal structures of the enzyme without substrate, bound to cellohexaose (substrate) or cellobiose (product), show the positioning of ligands to calcium and adjacent residues in the catalytic domain that may contribute to substrate binding and facilitate product release. We also investigated the properties of the enzyme engineered to contain an additional carbohydrate binding module (CBM3a). Relative to the catalytic domain alone, CBM3a gave improved binding for Avicel (a crystalline form of cellulose), and catalytic efficiency (k
MeSH term(s)	Calcium/metabolism ; Catalytic Domain ; Cellulase/chemistry ; Cellulase/metabolism ; Cellulose/chemistry ; Cellulose/metabolism ; Substrate Specificity ; Ligands ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Biocatalysis ; Protein Domains
Chemical Substances	Calcium (SY7Q814VUP) ; Cellulase (EC 3.2.1.4) ; Cellulose (9004-34-6) ; Ligands ; Bacterial Proteins
Language	English
Publishing date	2023-03-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.104655
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Article ; Online: Spectroscopic investigation of iron(III) cysteamine dioxygenase in the presence of substrate (analogs): implications for the nature of substrate-bound reaction intermediates.

Fernandez, Rebeca L / Juntunen, Nicholas D / Fox, Brian G / Brunold, Thomas C

Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry

2021 Volume 26, Issue 8, Page(s) 947–955

Abstract: Thiol dioxygenases (TDOs) are a class of metalloenzymes that oxidize various thiol-containing substrates to their corresponding sulfinic acids. Originally established by X-ray crystallography for cysteine dioxygenase (CDO), all TDOs are believed to ... ...

Abstract	Thiol dioxygenases (TDOs) are a class of metalloenzymes that oxidize various thiol-containing substrates to their corresponding sulfinic acids. Originally established by X-ray crystallography for cysteine dioxygenase (CDO), all TDOs are believed to contain a 3-histidine facial triad that coordinates the necessary Fe(II) cofactor. However, very little additional information is available for cysteamine dioxygenase (ADO), the only other mammalian TDO besides CDO. Previous spectroscopic characterizations revealed that ADO likely binds substrate cysteamine in a monodentate fashion, while a mass spectrometry study provided evidence that a thioether crosslink can form between Cys206 and Tyr208 (mouse ADO numbering). In the present study, we have used electronic absorption and electron paramagnetic resonance (EPR) spectroscopies to investigate the species formed upon incubation of Fe(III)ADO with sulfhydryl-containing substrates and the superoxide surrogates azide and cyanide. Our data reveal that azide is unable to coordinate to cysteamine-bound Fe(III)ADO, suggesting that the Fe(III) center lacks an open coordination site or azide competes with cysteamine for the same binding site. Alternatively, cyanide binds to either cysteamine- or Cys-bound Fe(III)ADO to yield a low-spin (S = 1/2) EPR signal that is distinct from that observed for cyanide/Cys-bound Fe(III)CDO, revealing differences in the active-site pockets between ADO and CDO. Finally, EPR spectra obtained for cyanide/cysteamine adducts of wild-type Fe(III)ADO and its Tyr208Phe variant are superimposable, implying that either an insignificant fraction of as-isolated wild-type enzyme is crosslinked or that formation of the thioether bond has minimal effects on the electronic structure of the iron cofactor.
MeSH term(s)	Animals ; Cysteine Dioxygenase ; Dioxygenases ; Electron Spin Resonance Spectroscopy ; Iron ; Mice
Chemical Substances	Iron (E1UOL152H7) ; Dioxygenases (EC 1.13.11.-) ; cysteamine dioxygenase (EC 1.13.11.19) ; Cysteine Dioxygenase (EC 1.13.11.20)
Language	English
Publishing date	2021-09-27
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1464026-0
ISSN	1432-1327 ; 0949-8257
ISSN (online)	1432-1327
ISSN	0949-8257
DOI	10.1007/s00775-021-01904-5
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Article ; Online: Multifunctional cellulases are potent, versatile tools for a renewable bioeconomy.

Glasgow, Evan / Vander Meulen, Kirk / Kuch, Nate / Fox, Brian G

Current opinion in biotechnology

2021 Volume 67, Page(s) 141–148

Abstract: Enzyme performance is critical to the future bioeconomy based on renewable plant materials. Plant biomass can be efficiently hydrolyzed by multifunctional cellulases (MFCs) into sugars suitable for conversion into fuels and chemicals, and MFCs fall into ... ...

Abstract	Enzyme performance is critical to the future bioeconomy based on renewable plant materials. Plant biomass can be efficiently hydrolyzed by multifunctional cellulases (MFCs) into sugars suitable for conversion into fuels and chemicals, and MFCs fall into three functional categories. Recent work revealed MFCs with broad substrate specificity, dual exo-activity/endo-activity on cellulose, and intramolecular synergy, among other novel characteristics. Binding modules and accessory catalytic domains amplify MFC and xylanase activity in a wide variety of ways, and processive endoglucanases achieve autosynergy on cellulose. Multidomain MFCs from Caldicellulosiruptor are heat-tolerant, adaptable to variable cellulose crystallinity, and may provide interchangeable scaffolds for recombinant design. Further studies of MFC properties and their reactivity with plant biomass are recommended for increasing biorefinery yields.
MeSH term(s)	Biomass ; Cellulase/metabolism ; Cellulases ; Cellulose ; Substrate Specificity
Chemical Substances	Cellulose (9004-34-6) ; Cellulases (EC 3.2.1.-) ; Cellulase (EC 3.2.1.4)
Language	English
Publishing date	2021-02-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	1052045-4
ISSN	1879-0429 ; 0958-1669
ISSN (online)	1879-0429
ISSN	0958-1669
DOI	10.1016/j.copbio.2020.12.020
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Article ; Online: A broad specificity β-propeller enzyme from Rhodopseudomonas palustris that hydrolyzes many lactones including γ-valerolactone.

Hall, Benjamin W / Bingman, Craig A / Fox, Brian G / Noguera, Daniel R / Donohue, Timothy J

The Journal of biological chemistry

2022 Volume 299, Issue 1, Page(s) 102782

Abstract: Lactones are prevalent in biological and industrial settings, yet there is a lack of information regarding enzymes used to metabolize these compounds. One compound, γ-valerolactone (GVL), is used as a solvent to dissolve plant cell walls into sugars and ... ...

Abstract	Lactones are prevalent in biological and industrial settings, yet there is a lack of information regarding enzymes used to metabolize these compounds. One compound, γ-valerolactone (GVL), is used as a solvent to dissolve plant cell walls into sugars and aromatic molecules for subsequent microbial conversion to fuels and chemicals. Despite the promise of GVL as a renewable solvent for biomass deconstruction, residual GVL can be toxic to microbial fermentation. Here, we identified a Ca
MeSH term(s)	Calcium ; Catalysis ; Lactones/chemistry ; Phylogeny ; Rhodopseudomonas ; Solvents/chemistry ; Substrate Specificity ; Water/chemistry
Chemical Substances	Calcium (SY7Q814VUP) ; gamma-valerolactone (O7056XK37X) ; Lactones ; Solvents ; Water (059QF0KO0R)
Language	English
Publishing date	2022-12-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2022.102782
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Article ; Online: SARM1 is responsible for calpain-dependent dendrite degeneration in mouse hippocampal neurons.

Miyamoto, Takashi / Kim, Chaeyoung / Chow, Johann / Dugas, Jason C / DeGroot, Jack / Bagdasarian, Alex L / Thottumkara, Arun P / Larhammar, Martin / Calvert, Meredith Ek / Fox, Brian M / Lewcock, Joseph W / Kane, Lesley A

The Journal of biological chemistry

2024 Volume 300, Issue 2, Page(s) 105630

Abstract: Sterile alpha and toll/interleukin receptor motif-containing 1 (SARM1) is a critical regulator of axon degeneration that acts through hydrolysis of ... ...

Abstract	Sterile alpha and toll/interleukin receptor motif-containing 1 (SARM1) is a critical regulator of axon degeneration that acts through hydrolysis of NAD
MeSH term(s)	Animals ; Mice ; Armadillo Domain Proteins/genetics ; Armadillo Domain Proteins/metabolism ; Axons/metabolism ; Calpain/metabolism ; Cytoskeletal Proteins/metabolism ; Dendrites/metabolism ; Neurons/metabolism ; Signal Transduction
Chemical Substances	Armadillo Domain Proteins ; Calpain (EC 3.4.22.-) ; Cytoskeletal Proteins ; SARM1 protein, mouse
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2024.105630
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Article ; Online: Discovery and Preclinical Activity of BMS-986351, an Antibody to SIRPα That Enhances Macrophage-mediated Tumor Phagocytosis When Combined with Opsonizing Antibodies.

Chan, Henry / Trout, Christina V / Mikolon, David / Adams, Preston / Guzman, Roberto / Mavrommatis, Konstantinos / Abbasian, Mahan / Hadjivassiliou, Haralambos / Dearth, Lawrence / Fox, Brian A / Sivakumar, Pallavur / Cho, Ho / Hariharan, Kandasamy

Cancer research communications

2024 Volume 4, Issue 2, Page(s) 505–515

Abstract: In normal cells, binding of the transmembrane protein CD47 to signal regulatory protein-α (SIRPα) on macrophages induces an antiphagocytic signal. Tumor cells hijack this pathway and overexpress CD47 to evade immune destruction. Macrophage antitumor ... ...

Abstract	In normal cells, binding of the transmembrane protein CD47 to signal regulatory protein-α (SIRPα) on macrophages induces an antiphagocytic signal. Tumor cells hijack this pathway and overexpress CD47 to evade immune destruction. Macrophage antitumor activity can be restored by simultaneously blocking the CD47-SIRPα signaling axis and inducing a prophagocytic signal via tumor-opsonizing antibodies. We identified a novel, fully human mAb (BMS-986351) that binds SIRPα with high affinity. BMS-986351 demonstrated broad binding coverage across SIRPα polymorphisms and potently blocked CD47-SIRPα binding at the CD47 binding site in a dose-dependent manner. In vitro, BMS-986351 increased phagocytic activity against cell lines from solid tumors and hematologic malignancies, and this effect was markedly enhanced when BMS-986351 was combined with the opsonizing antibodies cetuximab and rituximab. A phase I dose-escalation/-expansion study of BMS-986351 for the treatment of advanced solid and hematologic malignancies is underway (NCT03783403). Significance: Increasing the phagocytotic capabilities of tumor-associated macrophages by modulating macrophage-tumor cell surface signaling via the CD47-SIRPα axis is a novel strategy. Molecules targeting CD47 have potential but its ubiquitous expression necessitates higher therapeutic doses to overcome potential antigen sink effects. The restricted expression pattern of SIRPα may limit toxicities and lower doses of the SIRPα antibody BMS-986351 may overcome target mediated drug disposition while maintaining the desired pharmacology.
MeSH term(s)	Humans ; CD47 Antigen/genetics ; Receptors, Immunologic/genetics ; Phagocytosis ; Macrophages ; Neoplasms/drug therapy ; Antibodies, Neoplasm/metabolism ; Opsonin Proteins/metabolism ; Hematologic Neoplasms/metabolism
Chemical Substances	CD47 Antigen ; Receptors, Immunologic ; Antibodies, Neoplasm ; Opsonin Proteins
Language	English
Publishing date	2024-03-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2767-9764
ISSN (online)	2767-9764
DOI	10.1158/2767-9764.CRC-23-0634
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