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Article ; Online: Microbial biotechnology in the effort to end hunger.

Ramos, Juan Luis / Bernal, Patricia / Salvachúa, Davinia

2023 Volume 16, Issue 8, Page(s) 1581–1583

MeSH term(s)	Hunger ; Biotechnology
Language	English
Publishing date	2023-06-23
Publishing country	United States
Document type	Editorial ; Research Support, Non-U.S. Gov't
ZDB-ID	2406063-X
ISSN	1751-7915 ; 1751-7915
ISSN (online)	1751-7915
ISSN	1751-7915
DOI	10.1111/1751-7915.14295
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Article ; Online: Systems biology-guided understanding of white-rot fungi for biotechnological applications: A review.

Kijpornyongpan, Teeratas / Schwartz, Alexa / Yaguchi, Allison / Salvachúa, Davinia

iScience

2022 Volume 25, Issue 7, Page(s) 104640

Abstract: Plant-derived biomass is the most abundant biogenic carbon source on Earth. Despite this, only a small clade of organisms known as white-rot fungi (WRF) can efficiently break down both the polysaccharide and lignin components of plant cell walls. This ... ...

Abstract	Plant-derived biomass is the most abundant biogenic carbon source on Earth. Despite this, only a small clade of organisms known as white-rot fungi (WRF) can efficiently break down both the polysaccharide and lignin components of plant cell walls. This unique ability imparts a key role for WRF in global carbon cycling and highlights their potential utilization in diverse biotechnological applications. To date, research on WRF has primarily focused on their extracellular 'digestive enzymes' whereas knowledge of their intracellular metabolism remains underexplored. Systems biology is a powerful approach to elucidate biological processes in numerous organisms, including WRF. Thus, here we review systems biology methods applied to WRF to date, highlight observations related to their intracellular metabolism, and conduct comparative extracellular proteomic analyses to establish further correlations between WRF species, enzymes, and cultivation conditions. Lastly, we discuss biotechnological opportunities of WRF as well as challenges and future research directions.
Language	English
Publishing date	2022-06-18
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2022.104640
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Article: Burkholderia: An Untapped but Promising Bacterial Genus for the Conversion of Aromatic Compounds

Morya, Raj / Salvachúa, Davinia / Thakur, Indu Shekhar

Trends in biotechnology. 2020,

2020

Abstract: Burkholderia, a bacterial genus comprising more than 120 species, is typically reported to inhabit soil and water environments. These Gram-negative bacteria harbor a variety of aromatic catabolic pathways and are thus potential organisms for ... ...

Abstract	Burkholderia, a bacterial genus comprising more than 120 species, is typically reported to inhabit soil and water environments. These Gram-negative bacteria harbor a variety of aromatic catabolic pathways and are thus potential organisms for bioremediation of sites contaminated with aromatic pollutants. However, there are still substantial gaps in our knowledge of these catabolic processes that must be filled before these pathways and organisms can be harnessed for biotechnological applications. This review presents recent discoveries on the catabolism of monoaromatic and polycyclic aromatic hydrocarbons, as well as of heterocyclic compounds, by a diversity of Burkholderia strains. We also present a perspective on the beneficial features of Burkholderia spp. and future directions for their potential utilization in the bioremediation and bioconversion of aromatic compounds.
Keywords	Burkholderia ; Gram-negative bacteria ; biochemical pathways ; bioremediation ; biotransformation ; heterocyclic compounds ; metabolism ; pollutants ; polycyclic aromatic hydrocarbons ; soil
Language	English
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
ZDB-ID	47474-5
ISSN	1879-3096 ; 0167-7799
ISSN (online)	1879-3096
ISSN	0167-7799
DOI	10.1016/j.tibtech.2020.02.008
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Article ; Online: Burkholderia: An Untapped but Promising Bacterial Genus for the Conversion of Aromatic Compounds.

Morya, Raj / Salvachúa, Davinia / Thakur, Indu Shekhar

Trends in biotechnology

2020 Volume 38, Issue 9, Page(s) 963–975

Abstract	Burkholderia, a bacterial genus comprising more than 120 species, is typically reported to inhabit soil and water environments. These Gram-negative bacteria harbor a variety of aromatic catabolic pathways and are thus potential organisms for bioremediation of sites contaminated with aromatic pollutants. However, there are still substantial gaps in our knowledge of these catabolic processes that must be filled before these pathways and organisms can be harnessed for biotechnological applications. This review presents recent discoveries on the catabolism of monoaromatic and polycyclic aromatic hydrocarbons, as well as of heterocyclic compounds, by a diversity of Burkholderia strains. We also present a perspective on the beneficial features of Burkholderia spp. and future directions for their potential utilization in the bioremediation and bioconversion of aromatic compounds.
MeSH term(s)	Biodegradation, Environmental ; Burkholderia/genetics ; Burkholderia/metabolism ; Organic Chemicals/metabolism ; Organic Chemicals/toxicity ; Polycyclic Aromatic Hydrocarbons/metabolism ; Polycyclic Aromatic Hydrocarbons/toxicity ; Soil Microbiology ; Soil Pollutants/metabolism ; Soil Pollutants/toxicity
Chemical Substances	Organic Chemicals ; Polycyclic Aromatic Hydrocarbons ; Soil Pollutants
Language	English
Publishing date	2020-03-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	47474-5
ISSN	1879-3096 ; 0167-7799
ISSN (online)	1879-3096
ISSN	0167-7799
DOI	10.1016/j.tibtech.2020.02.008
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Article ; Online: Current trends in waste valorization.

Rene, Eldon R / Sarangi, Prakash K / Sànchez I Nogué, Violeta / Schnürer, Anna / Salvachúa, Davinia

Microbial biotechnology

2022 Volume 16, Issue 2, Page(s) 173–176

Abstract: This paper presents the scientific breakthroughs made in bioprocess engineering and microbial biotechnology for the conversion of wastes into products with added value and/or biofuels. The significant results obtained in the emerging fields of hybrid ... ...

Abstract	This paper presents the scientific breakthroughs made in bioprocess engineering and microbial biotechnology for the conversion of wastes into products with added value and/or biofuels. The significant results obtained in the emerging fields of hybrid electrosynthesis, the role of enzymes in the degradation of plastics, polyhydroxyalkanoate and 5-aminolevulinic acid production, fermentation technology and the application of molecular engineering tools to bioprocess technology are highlighted.
MeSH term(s)	Biotechnology/methods ; Fermentation ; Polyhydroxyalkanoates ; Biofuels
Chemical Substances	Polyhydroxyalkanoates ; Biofuels
Language	English
Publishing date	2022-12-21
Publishing country	United States
Document type	Editorial
ZDB-ID	2406063-X
ISSN	1751-7915 ; 1751-7915
ISSN (online)	1751-7915
ISSN	1751-7915
DOI	10.1111/1751-7915.14198
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Article ; Online: Comparison of wild-type KT2440 and genome-reduced EM42 Pseudomonas putida strains for muconate production from aromatic compounds and glucose.

Amendola, Caroline R / Cordell, William T / Kneucker, Colin M / Szostkiewicz, Caralyn J / Ingraham, Morgan A / Monninger, Michela / Wilton, Rosemarie / Pfleger, Brian F / Salvachúa, Davinia / Johnson, Christopher W / Beckham, Gregg T

Metabolic engineering

2023 Volume 81, Page(s) 88–99

Abstract: Pseudomonas putida KT2440 is a robust, aromatic catabolic bacterium that has been widely engineered to convert bio-based and waste-based feedstocks to target products. Towards industrial domestication of P. putida KT2440, rational genome reduction has ... ...

Abstract	Pseudomonas putida KT2440 is a robust, aromatic catabolic bacterium that has been widely engineered to convert bio-based and waste-based feedstocks to target products. Towards industrial domestication of P. putida KT2440, rational genome reduction has been previously conducted, resulting in P. putida strain EM42, which exhibited characteristics that could be advantageous for production strains. Here, we compared P. putida KT2440- and EM42-derived strains for cis,cis-muconic acid production from an aromatic compound, p-coumarate, and in separate strains, from glucose. To our surprise, the EM42-derived strains did not outperform the KT2440-derived strains in muconate production from either substrate. In bioreactor cultivations, KT2440- and EM42-derived strains produced muconate from p-coumarate at titers of 45 g/L and 37 g/L, respectively, and from glucose at 20 g/L and 13 g/L, respectively. To provide additional insights about the differences in the parent strains, we analyzed growth profiles of KT2440 and EM42 on aromatic compounds as the sole carbon and energy sources. In general, the EM42 strain exhibited reduced growth rates but shorter growth lags than KT2440. We also observed that EM42-derived strains resulted in higher growth rates on glucose compared to KT2440-derived strains, but only at the lowest glucose concentrations tested. Transcriptomics revealed that genome reduction in EM42 had global effects on transcript levels and showed that the EM42-derived strains that produce muconate from glucose exhibit reduced modulation of gene expression in response to changes in glucose concentrations. Overall, our results highlight that additional studies are warranted to understand the effects of genome reduction on microbial metabolism and physiology, especially when intended for use in production strains.
MeSH term(s)	Pseudomonas putida/genetics ; Pseudomonas putida/metabolism ; Glucose/metabolism ; Bioreactors
Chemical Substances	Glucose (IY9XDZ35W2)
Language	English
Publishing date	2023-11-23
Publishing country	Belgium
Document type	Journal Article
ZDB-ID	1470383-x
ISSN	1096-7184 ; 1096-7176
ISSN (online)	1096-7184
ISSN	1096-7176
DOI	10.1016/j.ymben.2023.11.004
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Article: Particle Size Reduction of Poly(ethylene terephthalate) Increases the Rate of Enzymatic Depolymerization But Does Not Increase the Overall Conversion Extent

Brizendine, Richard K. / Erickson, Erika / Haugen, Stefan J. / Ramirez, Kelsey J. / Miscall, Joel / Salvachúa, Davinia / Pickford, Andrew R. / Sobkowicz, Margaret J. / McGeehan, John E. / Beckham, Gregg T.

ACS sustainable chemistry & engineering. 2022 July 07, v. 10, no. 28

2022

Abstract: Enzymatic depolymerization of poly(ethylene terephthalate) (PET) has emerged as a potential method for PET recycling, but extensive thermomechanical preprocessing to reduce both the crystallinity and particle size of PET is often conducted, which is ... ...

Abstract	Enzymatic depolymerization of poly(ethylene terephthalate) (PET) has emerged as a potential method for PET recycling, but extensive thermomechanical preprocessing to reduce both the crystallinity and particle size of PET is often conducted, which is costly and energy-intensive. In the current work, we use high-crystallinity PET (HC-PET) and low-crystallinity cryomilled PET (CM-PET) with three distinct particle size distributions to investigate the effect of PET particle size and crystallinity on the performance of a variant of the leaf compost-cutinase enzyme (LCC-ICCG). We show that LCC-ICCG hydrolyzes PET, resulting in the accumulation of terephthalic acid and, interestingly, also releases significant amount of mono(2-hydroxyethyl)terephthalate. Particle size reduction of PET increased the maximum rate of reaction for HC-PET, while the maximum hydrolysis rate for CM-PET was not significantly different across particle sizes. For both substrates, however, we show that particle size reduction has little effect on the overall conversion extent. Specifically, the CM-PET film was converted to 99 ± 0.2% mass loss within 48 h, while the HC-PET powder reached only 23.5 ± 0.0% conversion in 144 h. Overall, these results suggest that amorphization of PET is a necessary pretreatment step for enzymatic PET recycling using the LCC-ICCG enzyme but that particle size reduction may not be required.
Keywords	crystal structure ; depolymerization ; enzymes ; green chemistry ; hydrolysis ; leaves ; particle size
Language	English
Dates of publication	2022-0707
Size	p. 9131-9140.
Publishing place	American Chemical Society
Document type	Article
ISSN	2168-0485
DOI	10.1021/acssuschemeng.2c01961
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Article ; Online: Lignin conversion to β-ketoadipic acid by

Werner, Allison Z / Cordell, William T / Lahive, Ciaran W / Klein, Bruno C / Singer, Christine A / Tan, Eric C D / Ingraham, Morgan A / Ramirez, Kelsey J / Kim, Dong Hyun / Pedersen, Jacob Nedergaard / Johnson, Christopher W / Pfleger, Brian F / Beckham, Gregg T / Salvachúa, Davinia

Science advances

2023 Volume 9, Issue 36, Page(s) eadj0053

Abstract: Bioconversion of a heterogeneous mixture of lignin-related aromatic compounds (LRCs) to a single product via microbial biocatalysts is a promising approach to valorize lignin. Here, ...

Abstract	Bioconversion of a heterogeneous mixture of lignin-related aromatic compounds (LRCs) to a single product via microbial biocatalysts is a promising approach to valorize lignin. Here,
MeSH term(s)	Metabolic Engineering ; Lignin ; Pseudomonas putida/genetics ; Carbon
Chemical Substances	3-oxoadipic acid (1379JRA56F) ; Lignin (9005-53-2) ; Carbon (7440-44-0)
Language	English
Publishing date	2023-09-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adj0053
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Article ; Online: Elastomeric vitrimers from designer polyhydroxyalkanoates with recyclability and biodegradability.

Cywar, Robin M / Ling, Chen / Clarke, Ryan W / Kim, Dong Hyun / Kneucker, Colin M / Salvachúa, Davinia / Addison, Bennett / Hesse, Sarah A / Takacs, Christopher J / Xu, Shu / Demirtas, Meltem Urgun / Woodworth, Sean P / Rorrer, Nicholas A / Johnson, Christopher W / Tassone, Christopher J / Allen, Robert D / Chen, Eugene Y-X / Beckham, Gregg T

Science advances

2023 Volume 9, Issue 47, Page(s) eadi1735

Abstract: Cross-linked elastomers are stretchable materials that typically are not recyclable or biodegradable. Medium-chain-length polyhydroxyalkanoates (mcl-PHAs) are soft and ductile, making these bio-based polymers good candidates for biodegradable elastomers. ...

Abstract	Cross-linked elastomers are stretchable materials that typically are not recyclable or biodegradable. Medium-chain-length polyhydroxyalkanoates (mcl-PHAs) are soft and ductile, making these bio-based polymers good candidates for biodegradable elastomers. Elasticity is commonly imparted by a cross-linked network structure, and covalent adaptable networks have emerged as a solution to prepare recyclable thermosets via triggered rearrangement of dynamic covalent bonds. Here, we develop biodegradable and recyclable elastomers by chemically installing the covalent adaptable network within biologically produced mcl-PHAs. Specifically, an engineered strain of
MeSH term(s)	Polyhydroxyalkanoates/chemistry ; Pseudomonas putida/genetics ; Elasticity ; Elastomers
Chemical Substances	Polyhydroxyalkanoates ; Elastomers
Language	English
Publishing date	2023-11-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adi1735
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Article ; Online: Production of itaconic acid from alkali pretreated lignin by dynamic two stage bioconversion.

Elmore, Joshua R / Dexter, Gara N / Salvachúa, Davinia / Martinez-Baird, Jessica / Hatmaker, E Anne / Huenemann, Jay D / Klingeman, Dawn M / Peabody, George L / Peterson, Darren J / Singer, Christine / Beckham, Gregg T / Guss, Adam M

Nature communications

2021 Volume 12, Issue 1, Page(s) 2261

Abstract: Expanding the portfolio of products that can be made from lignin will be critical to enabling a viable bio-based economy. Here, we engineer Pseudomonas putida for high-yield production of the tricarboxylic acid cycle-derived building block chemical, ... ...

Abstract	Expanding the portfolio of products that can be made from lignin will be critical to enabling a viable bio-based economy. Here, we engineer Pseudomonas putida for high-yield production of the tricarboxylic acid cycle-derived building block chemical, itaconic acid, from model aromatic compounds and aromatics derived from lignin. We develop a nitrogen starvation-detecting biosensor for dynamic two-stage bioproduction in which itaconic acid is produced during a non-growth associated production phase. Through the use of two distinct itaconic acid production pathways, the tuning of TCA cycle gene expression, deletion of competing pathways, and dynamic regulation, we achieve an overall maximum yield of 56% (mol/mol) and titer of 1.3 g/L from p-coumarate, and 1.4 g/L titer from monomeric aromatic compounds produced from alkali-treated lignin. This work illustrates a proof-of-principle that using dynamic metabolic control to reroute carbon after it enters central metabolism enables production of valuable chemicals from lignin at high yields by relieving the burden of constitutively expressing toxic heterologous pathways.
MeSH term(s)	Alkalies/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Basidiomycota/enzymology ; Basidiomycota/genetics ; Biosensing Techniques ; Burkholderia/enzymology ; Burkholderia/genetics ; Carbon/metabolism ; Citric Acid Cycle/genetics ; Coumaric Acids/metabolism ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Industrial Microbiology/methods ; Lignin/chemistry ; Lignin/metabolism ; Metabolic Engineering/methods ; Proof of Concept Study ; Pseudomonas putida/genetics ; Pseudomonas putida/metabolism ; Succinates/metabolism
Chemical Substances	Alkalies ; Bacterial Proteins ; Coumaric Acids ; Fungal Proteins ; Succinates ; Carbon (7440-44-0) ; Lignin (9005-53-2) ; p-coumaric acid (IBS9D1EU3J) ; itaconic acid (Q4516562YH)
Language	English
Publishing date	2021-04-15
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-22556-8
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